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Journal articles on the topic 'Accurate Alignment of Short Reads'

Author: Grafiati

Published: 6 September 2023

Last updated: 31 July 2025

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1

Carter, John Lawrence, Harlan Stevens, Perry G. Ridge, and Steven Michael Johnson. "Short Sequence Aligner Benchmarking for Chromatin Research." International Journal of Molecular Sciences 24, no. 18 (2023): 14074. http://dx.doi.org/10.3390/ijms241814074.

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Much of today’s molecular science revolves around next-generation sequencing. Frequently, the first step in analyzing such data is aligning sequencing reads to a reference genome. This step is often taken for granted, but any analysis downstream of the alignment will be affected by the aligner’s ability to correctly map sequences. In most cases, for research into chromatin structure and nucleosome positioning, ATAC-seq, ChIP-seq, and MNase-seq experiments use short read lengths. How well aligners manage these reads is critical. Most aligner programs will output mapped reads and unmapped reads.

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Asghari, Hossein, Yen-Yi Lin, Yang Xu, Ehsan Haghshenas, Colin C. Collins, and Faraz Hach. "CircMiner: accurate and rapid detection of circular RNA through splice-aware pseudo-alignment scheme." Bioinformatics 36, no. 12 (2020): 3703–11. http://dx.doi.org/10.1093/bioinformatics/btaa232.

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Abstract Motivation The ubiquitous abundance of circular RNAs (circRNAs) has been revealed by performing high-throughput sequencing in a variety of eukaryotes. circRNAs are related to some diseases, such as cancer in which they act as oncogenes or tumor-suppressors and, therefore, have the potential to be used as biomarkers or therapeutic targets. Accurate and rapid detection of circRNAs from short reads remains computationally challenging. This is due to the fact that identifying chimeric reads, which is essential for finding back-splice junctions, is a complex process. The sensitivity of dis

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Mkrtchian, A. A., K. S. Grammatikati, P. G. Kazakova, et al. "Comparative Analysis of Structural Variant Callers on the Short-Read Whole-Genome Sequencing Data." Генетика 59, no. 6 (2023): 687–707. http://dx.doi.org/10.31857/s0016675823060115.

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In this study three structural variant callers (Manta, Smoove, Delly) were analysed on the whole-genome sequencing data using four different alignment algorithms: DRAGEN, GDC DNA-Seq Alignment Workflow, GDC DNA-Seq Alignment Workflow + GDC DNA-Seq Co-Cleaning Workflow, NovoAlign, different lengths of raw reads: 2 × 150 bp and 2 × 250 bp, different mean genome coverage values. Results were compared to etalon results of GIAB team. Structural variants validation was hold also with Sanger sequencing. Structural variants deletions and insertions as it turned out were best determined with Manta tool

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Kumar, Sanjeev, Suneeta Agarwal, and Ranvijay. "Fast and memory efficient approach for mapping NGS reads to a reference genome." Journal of Bioinformatics and Computational Biology 17, no. 02 (2019): 1950008. http://dx.doi.org/10.1142/s0219720019500082.

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New generation sequencing machines: Illumina and Solexa can generate millions of short reads from a given genome sequence on a single run. Alignment of these reads to a reference genome is a core step in Next-generation sequencing data analysis such as genetic variation and genome re-sequencing etc. Therefore there is a need of a new approach, efficient with respect to memory as well as time to align these enormous reads with the reference genome. Existing techniques such as MAQ, Bowtie, BWA, BWBBLE, Subread, Kart, and Minimap2 require huge memory for whole reference genome indexing and reads

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Flouri, Tomas, Costas S. Iliopoulos, Solon P. Pissis, and German Tischler. "Mapping Short Reads to a Genomic Sequence with Circular Structure." International Journal of Systems Biology and Biomedical Technologies 1, no. 1 (2012): 26–34. http://dx.doi.org/10.4018/ijsbbt.2012010103.

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Constant advances in DNA sequencing technologies are turning whole-genome sequencing into a routine procedure, resulting in massive amounts of data that need to be processed. Tens of gigabytes of data, in the form of short sequences (reads), need to be mapped back onto reference sequences, a few gigabases long. A first generation of short-read alignment algorithms successfully employed hash tables, and the current second generation uses the Burrows-Wheeler transform, further improving speed and memory footprint. These next-generation sequencing technologies allow researchers to characterise a

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Teixeira, Andreia Sofia, Francisco Fernandes, and Alexandre P. Francisco. "SpliceTAPyR — An Efficient Method for Transcriptome Alignment." International Journal of Foundations of Computer Science 29, no. 08 (2018): 1297–310. http://dx.doi.org/10.1142/s0129054118430049.

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RNA-Seq is a Next-Generation Sequencing (NGS) protocol for sequencing the messenger RNA in a cell and generates millions of short sequence fragments, reads, in a single run. These reads can be used to measure levels of gene expression and to identify novel splice variants of genes. One of the critical steps in an RNA-Seq experiment is mapping NGS reads to the reference genome. Because RNA-Seq reads can span over more than one exon in the genome, this task is challenging. In the last decade, tools for RNA-Seq alignment have emerged, but most of them run in two phases. First, the pipeline only m

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Ebler, Jana, Peter Ebert, Wayne E. Clarke, et al. "Pangenome-based genome inference allows efficient and accurate genotyping across a wide spectrum of variant classes." Nature Genetics 54, no. 4 (2022): 518–25. http://dx.doi.org/10.1038/s41588-022-01043-w.

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AbstractTypical genotyping workflows map reads to a reference genome before identifying genetic variants. Generating such alignments introduces reference biases and comes with substantial computational burden. Furthermore, short-read lengths limit the ability to characterize repetitive genomic regions, which are particularly challenging for fast k-mer-based genotypers. In the present study, we propose a new algorithm, PanGenie, that leverages a haplotype-resolved pangenome reference together with k-mer counts from short-read sequencing data to genotype a wide spectrum of genetic variation—a pr

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Li, H., and R. Durbin. "Fast and accurate short read alignment with Burrows-Wheeler transform." Bioinformatics 25, no. 14 (2009): 1754–60. http://dx.doi.org/10.1093/bioinformatics/btp324.

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MAURER-STROH, SEBASTIAN, VITHIAGARAN GUNALAN, WING-CHEONG WONG, and FRANK EISENHABER. "A SIMPLE SHORTCUT TO UNSUPERVISED ALIGNMENT-FREE PHYLOGENETIC GENOME GROUPINGS, EVEN FROM UNASSEMBLED SEQUENCING READS." Journal of Bioinformatics and Computational Biology 11, no. 06 (2013): 1343005. http://dx.doi.org/10.1142/s0219720013430051.

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We propose an extension to alignment-free approaches that can produce reasonably accurate phylogenetic groupings starting from unaligned genomes, for example, as fast as 1 min on a standard desktop computer for 25 bacterial genomes. A 6-fold speed-up and 11-fold reduction in memory requirements compared to previous alignment-free methods is achieved by reducing the comparison space to a representative sample of k-mers of optimal length and with specific tag motifs. This approach was applied to the test case of fitting the enterohemorrhagic O104:H4 E.coli strain from the 2011 outbreak in German

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Ghoneimy, Samy, and Samir Abou El-Seoud. "A MapReduce Framework for DNA Sequencing Data Processing." International Journal of Recent Contributions from Engineering, Science & IT (iJES) 4, no. 4 (2016): 11. http://dx.doi.org/10.3991/ijes.v4i4.6537.

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<p class="Els-1storder-head">Genomics and Next Generation Sequencers (NGS) like Illumina Hiseq produce data in the order of ‎‎200 billion base pairs in a single one-week run for a 60x human genome coverage, which ‎requires modern high-throughput experimental technologies that can ‎only be tackled with high performance computing (HPC) and specialized software algorithms called ‎‎“short read aligners”. This paper focuses on the implementation of the DNA sequencing as a set of MapReduce programs that will accept a DNA data set as a FASTQ file and finally generate a VCF (variant call format)

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Prodanov, Timofey, and Vikas Bansal. "Sensitive alignment using paralogous sequence variants improves long-read mapping and variant calling in segmental duplications." Nucleic Acids Research 48, no. 19 (2020): e114-e114. http://dx.doi.org/10.1093/nar/gkaa829.

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Abstract The ability to characterize repetitive regions of the human genome is limited by the read lengths of short-read sequencing technologies. Although long-read sequencing technologies such as Pacific Biosciences (PacBio) and Oxford Nanopore Technologies can potentially overcome this limitation, long segmental duplications with high sequence identity pose challenges for long-read mapping. We describe a probabilistic method, DuploMap, designed to improve the accuracy of long-read mapping in segmental duplications. It analyzes reads mapped to segmental duplications using existing long-read a

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Teng, Carolina, Renan Weege Achjian, Jiang Chau Wang, and Fernando Josepetti Fonseca. "Adapting the GACT-X Aligner to Accelerate Minimap2 in an FPGA Cloud Instance." Applied Sciences 13, no. 7 (2023): 4385. http://dx.doi.org/10.3390/app13074385.

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In genomic analysis, long reads are an emerging type of data processed by assembly algorithms to recover the complete genome sample. They are, on average, one or two orders of magnitude longer than short reads from the previous generation, which provides important advantages in information quality. However, longer sequences bring new challenges to computer processing, undermining the performance of assembly algorithms developed for short reads. This issue is amplified by the exponential growth of genetic data generation and by the slowdown of transistor technology progress, illustrated by Moor

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Al-Absi, Ahmed Abdulhakim, and Dae-Ki Kang. "Long Read Alignment with Parallel MapReduce Cloud Platform." BioMed Research International 2015 (2015): 1–13. http://dx.doi.org/10.1155/2015/807407.

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Genomic sequence alignment is an important technique to decode genome sequences in bioinformatics. Next-Generation Sequencing technologies produce genomic data of longer reads. Cloud platforms are adopted to address the problems arising from storage and analysis of large genomic data. Existing genes sequencing tools for cloud platforms predominantly consider short read gene sequences and adopt the Hadoop MapReduce framework for computation. However, serial execution of map and reduce phases is a problem in such systems. Therefore, in this paper, we introduce Burrows-Wheeler Aligner’s Smith-Wat

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Marin, Wesley M., Ravi Dandekar, Danillo G. Augusto, et al. "High-throughput Interpretation of Killer-cell Immunoglobulin-like Receptor Short-read Sequencing Data with PING." PLOS Computational Biology 17, no. 8 (2021): e1008904. http://dx.doi.org/10.1371/journal.pcbi.1008904.

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The killer-cell immunoglobulin-like receptor (KIR) complex on chromosome 19 encodes receptors that modulate the activity of natural killer cells, and variation in these genes has been linked to infectious and autoimmune disease, as well as having bearing on pregnancy and transplant outcomes. The medical relevance and high variability of KIR genes makes short-read sequencing an attractive technology for interrogating the region, providing a high-throughput, high-fidelity sequencing method that is cost-effective. However, because this gene complex is characterized by extensive nucleotide polymor

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Magdy Mohamed Abdelaziz Barakat, Sherif, Roselina Sallehuddin, Siti Sophiayati Yuhaniz, Raja Farhana R. Khairuddin, and Yasir Mahmood. "Genome assembly composition of the String “ACGT” array: a review of data structure accuracy and performance challenges." PeerJ Computer Science 9 (July 13, 2023): e1180. http://dx.doi.org/10.7717/peerj-cs.1180.

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Background The development of sequencing technology increases the number of genomes being sequenced. However, obtaining a quality genome sequence remains a challenge in genome assembly by assembling a massive number of short strings (reads) with the presence of repetitive sequences (repeats). Computer algorithms for genome assembly construct the entire genome from reads in two approaches. The de novo approach concatenates the reads based on the exact match between their suffix-prefix (overlapping). Reference-guided approach orders the reads based on their offsets in a well-known reference geno

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Mukherjee, Kingshuk, Bahar Alipanahi, Tamer Kahveci, Leena Salmela, and Christina Boucher. "Aligning optical maps to de Bruijn graphs." Bioinformatics 35, no. 18 (2019): 3250–56. http://dx.doi.org/10.1093/bioinformatics/btz069.

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Abstract Motivation Optical maps are high-resolution restriction maps (Rmaps) that give a unique numeric representation to a genome. Used in concert with sequence reads, they provide a useful tool for genome assembly and for discovering structural variations and rearrangements. Although they have been a regular feature of modern genome assembly projects, optical maps have been mainly used in post-processing step and not in the genome assembly process itself. Several methods have been proposed for pairwise alignment of single molecule optical maps—called Rmaps, or for aligning optical maps to a

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Wong, Thomas K. F., Teng Li, Louis Ranjard, Steven H. Wu, Jeet Sukumaran, and Allen G. Rodrigo. "An assembly-free method of phylogeny reconstruction using short-read sequences from pooled samples without barcodes." PLOS Computational Biology 17, no. 9 (2021): e1008949. http://dx.doi.org/10.1371/journal.pcbi.1008949.

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A current strategy for obtaining haplotype information from several individuals involves short-read sequencing of pooled amplicons, where fragments from each individual is identified by a unique DNA barcode. In this paper, we report a new method to recover the phylogeny of haplotypes from short-read sequences obtained using pooled amplicons from a mixture of individuals, without barcoding. The method, AFPhyloMix, accepts an alignment of the mixture of reads against a reference sequence, obtains the single-nucleotide-polymorphisms (SNP) patterns along the alignment, and constructs the phylogene

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Liu, Yongchao, Bernt Popp, and Bertil Schmidt. "CUSHAW3: Sensitive and Accurate Base-Space and Color-Space Short-Read Alignment with Hybrid Seeding." PLoS ONE 9, no. 1 (2014): e86869. http://dx.doi.org/10.1371/journal.pone.0086869.

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Tello, Daniel, Juanita Gil, Cristian D. Loaiza, John J. Riascos, Nicolás Cardozo, and Jorge Duitama. "NGSEP3: accurate variant calling across species and sequencing protocols." Bioinformatics 35, no. 22 (2019): 4716–23. http://dx.doi.org/10.1093/bioinformatics/btz275.

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Abstract Motivation Accurate detection, genotyping and downstream analysis of genomic variants from high-throughput sequencing data are fundamental features in modern production pipelines for genetic-based diagnosis in medicine or genomic selection in plant and animal breeding. Our research group maintains the Next-Generation Sequencing Experience Platform (NGSEP) as a precise, efficient and easy-to-use software solution for these features. Results Understanding that incorrect alignments around short tandem repeats are an important source of genotyping errors, we implemented in NGSEP new algor

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Musatov, I. Y., M. I. Sorokin, and А. A. Buzdin. "Bioinformatic approaches for detection of fusion genes and <i>trans</i>-splicing products." Биоорганическая химия 50, no. 3 (2024): 231–55. http://dx.doi.org/10.31857/s0132342324030033.

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Chimeric genes and transcripts can be biological markers as well as the reasons for tumor progression and development. Modern algorithms and high-throughput sequencing are the complementary clues to the question of the tumor origin and cancer detection as well as to the fundamental question of chimeric genes origin and their influence on molecular processes of the cell. A wide-range of algorithms for chimeric genes detection was developed, with various differences in computing speed, sensitivity, specificity, and focus on the experimental design. There exist three main types of bioinformatic a

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Chu, Wai Keung, Peter Edge, Ho Suk Lee, et al. "Ultraaccurate genome sequencing and haplotyping of single human cells." Proceedings of the National Academy of Sciences 114, no. 47 (2017): 12512–17. http://dx.doi.org/10.1073/pnas.1707609114.

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Accurate detection of variants and long-range haplotypes in genomes of single human cells remains very challenging. Common approaches require extensive in vitro amplification of genomes of individual cells using DNA polymerases and high-throughput short-read DNA sequencing. These approaches have two notable drawbacks. First, polymerase replication errors could generate tens of thousands of false-positive calls per genome. Second, relatively short sequence reads contain little to no haplotype information. Here we report a method, which is dubbed SISSOR (single-stranded sequencing using microflu

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Marin, Maximillian, Roger Vargas, Michael Harris, et al. "Benchmarking the empirical accuracy of short-read sequencing across the M. tuberculosis genome." Bioinformatics 38, no. 7 (2022): 1781–87. http://dx.doi.org/10.1093/bioinformatics/btac023.

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Abstract Motivation Short-read whole-genome sequencing (WGS) is a vital tool for clinical applications and basic research. Genetic divergence from the reference genome, repetitive sequences and sequencing bias reduces the performance of variant calling using short-read alignment, but the loss in recall and specificity has not been adequately characterized. To benchmark short-read variant calling, we used 36 diverse clinical Mycobacterium tuberculosis (Mtb) isolates dually sequenced with Illumina short-reads and PacBio long-reads. We systematically studied the short-read variant calling accurac

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Tapinos, Avraam, Bede Constantinides, My V. T. Phan, Samaneh Kouchaki, Matthew Cotten, and David L. Robertson. "The Utility of Data Transformation for Alignment, De Novo Assembly and Classification of Short Read Virus Sequences." Viruses 11, no. 5 (2019): 394. http://dx.doi.org/10.3390/v11050394.

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Advances in DNA sequencing technology are facilitating genomic analyses of unprecedented scope and scale, widening the gap between our abilities to generate and fully exploit biological sequence data. Comparable analytical challenges are encountered in other data-intensive fields involving sequential data, such as signal processing, in which dimensionality reduction (i.e., compression) methods are routinely used to lessen the computational burden of analyses. In this work, we explored the application of dimensionality reduction methods to numerically represent high-throughput sequence data for

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Linard, Benjamin, Krister Swenson, and Fabio Pardi. "Rapid alignment-free phylogenetic identification of metagenomic sequences." Bioinformatics 35, no. 18 (2019): 3303–12. http://dx.doi.org/10.1093/bioinformatics/btz068.

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Abstract Motivation Taxonomic classification is at the core of environmental DNA analysis. When a phylogenetic tree can be built as a prior hypothesis to such classification, phylogenetic placement (PP) provides the most informative type of classification because each query sequence is assigned to its putative origin in the tree. This is useful whenever precision is sought (e.g. in diagnostics). However, likelihood-based PP algorithms struggle to scale with the ever-increasing throughput of DNA sequencing. Results We have developed RAPPAS (Rapid Alignment-free Phylogenetic Placement via Ancest

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Prusokiene, Alisa, Neil Boonham, Adrian Fox, and Thomas P. Howard. "Mottle: Accurate pairwise substitution distance at high divergence through the exploitation of short-read mappers and gradient descent." PLOS ONE 19, no. 3 (2024): e0298834. http://dx.doi.org/10.1371/journal.pone.0298834.

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Current tools for estimating the substitution distance between two related sequences struggle to remain accurate at a high divergence. Difficulties at distant homologies, such as false seeding and over-alignment, create a high barrier for the development of a stable estimator. This is especially true for viral genomes, which carry a high rate of mutation, small size, and sparse taxonomy. Developing an accurate substitution distance measure would help to elucidate the relationship between highly divergent sequences, interrogate their evolutionary history, and better facilitate the discovery of

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Abde Aliy, Mohammed, Senbeta Bayeta, and Worku Takale. "Pacific bioscience sequence technology: Review." International Journal of Veterinary Science and Research 8, no. 1 (2022): 027–33. http://dx.doi.org/10.17352/ijvsr.000108.

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Pacific Biosciences has developed a platform that may sequence one molecule of DNA in a period via the polymerization of that strand with one enzyme. Single-molecule real-time sequencing by Pacific BioSciences’ technology is one of the most widely utilized third-generation sequencing technologies. PacBio single-molecule real-time Sequencing uses the Zero-mode waveguide’s ingenuity to distinguish the best fluorescence signal from the stable fluorescent backgrounds generated by disorganized free-floating nucleotides. PacBio single-molecule real-time sequencing does not require PCR amplification,

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Zhurbenko, Peter M., and Fedor N. Klimenko. "PhaseAll: a simple tool for read-based allele phasing." Ecological genetics 20, no. 1S (2022): 32. http://dx.doi.org/10.17816/ecogen112363.

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The currently used genome assembly algorithms do not provide for allele phasing. This can lead to the loss of important information about the genotype of diploid and polyploid individuals. Here we introduce PhaseAll, a simple tool for allele phasing based on short reads obtained by second-generation sequencing. As input data, the tool takes paired reeds in SAM format. PhaseAll iterates sequentially through each alignment position. When a polymorphic position (SNP, insertion or deletion) is first encountered, a unique mutation is written to each allele. For each subsequent polymorphic position,

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Elrick, Hillary, Jose Espejo Valle-Inclan, Katherine E. Trevers, et al. "Abstract LB080: SAVANA: a computational method to characterize structural variation in human cancer genomes using nanopore sequencing." Cancer Research 83, no. 8_Supplement (2023): LB080. http://dx.doi.org/10.1158/1538-7445.am2023-lb080.

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Abstract Whole-genome sequencing (WGS) of human cancers has revealed that structural variation, which refers to the rearrangement of the genome leading to the deletion, amplification of reshuffling of DNA segments ranging from a few hundred bp to entire chromosomes, is a key mutational process in cancer evolution. Notably, pan-cancer analyses have revealed that both simple and complex forms of structural variation are pervasive across diverse human cancers, and often underpin drug resistance and metastasis. To date, the study of cancer genomes has relied on the analysis of short-read WGS on th

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Sockell, Alexandra, Khi Pin Chua, Christopher Kingsley, et al. "Abstract 6624: Comprehensive, multi-omic detection of somatic variants from the GIAB HG008 matched tumor-normal pair using highly accurate long- and short-read whole-genome sequencing." Cancer Research 85, no. 8_Supplement_1 (2025): 6624. https://doi.org/10.1158/1538-7445.am2025-6624.

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Abstract Disentangling the molecular drivers of cancer progression requires a precise understanding of the somatic alterations that take place at the DNA level during tumor development. These include not only small changes like SNVs and indels, but also structural variants, changes in repetitive elements, differential methylation, as well as the haplotype context in which these changes occur. Existing short-read sequencing methods using sequencing by synthesis (SBS) chemistry lack the read length to characterize large structural variants or to span longer repetitive regions as well as to phase

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Atshemyan, Sofi, Andranik Chavushyan, Nerses Berberian, Arthur Sahakyan, Roksana Zakharyan, and Arsen Arakelyan. "Characterization of BRCA1/2 mutations in patients with family history of breast cancer in Armenia." F1000Research 6 (January 10, 2017): 29. http://dx.doi.org/10.12688/f1000research.10434.1.

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Background. Breast cancer is one of the most common cancers in women worldwide. The germline mutations of the BRCA1 and BRCA2 genes are the most significant and well characterized genetic risk factors for hereditary breast cancer. Intensive research in the last decades has demonstrated that the incidence of mutations varies widely among different populations. In this study we attempted to perform a pilot study for identification and characterization of mutations in BRCA1 and BRCA2 genes among Armenian patients with family history of breast cancer and their healthy relatives. Methods. We perfor

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Singh, Noor Pratap, Jamshed Khan, and Rob Patro. "Alevin-fry-atac enables rapid and memory frugal mapping of single-cell ATAC-seq data using virtual colors for accurate genomic pseudoalignment." Bioinformatics 41, Supplement_1 (2025): i237—i245. https://doi.org/10.1093/bioinformatics/btaf234.

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Abstract Summary Ultrafast mapping of short reads via lightweight mapping techniques such as pseudoalignment has significantly accelerated transcriptomic and metagenomic analyses with minimal accuracy loss compared to alignment-based methods. However, applying pseudoalignment to large genomic references, like chromosomes, is challenging due to their size and repetitive sequences. We introduce a new and modified pseudoalignment scheme that partitions each reference into “virtual colors.” These are essentially overlapping bins of fixed maximal extent on the reference sequences that are treated a

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Olawoye, Idowu B., Simon D. W. Frost, and Christian T. Happi. "The Bacteria Genome Pipeline (BAGEP): an automated, scalable workflow for bacteria genomes with Snakemake." PeerJ 8 (October 27, 2020): e10121. http://dx.doi.org/10.7717/peerj.10121.

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Next generation sequencing technologies are becoming more accessible and affordable over the years, with entire genome sequences of several pathogens being deciphered in few hours. However, there is the need to analyze multiple genomes within a short time, in order to provide critical information about a pathogen of interest such as drug resistance, mutations and genetic relationship of isolates in an outbreak setting. Many pipelines that currently do this are stand-alone workflows and require huge computational requirements to analyze multiple genomes. We present an automated and scalable pip

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Yun, Hyeongseok, Seungho Lee, Seunghyun Lim, et al. "Microbial Forensics: Comparison of MLVA Results According to NGS Methods, and Forensic DNA Analysis Using MLVA." Journal of the Korea Institute of Military Science and Technology 27, no. 4 (2024): 507–15. http://dx.doi.org/10.9766/kimst.2024.27.4.507.

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Microbial forensics is a scientific discipline for analyzing evidence related to biological crimes by identifying the origin of microorganisms. Multiple locus variable number tandem repeat analysis(MLVA) is one of the microbiological analysis methods used to specify subtypes within a species based on the number of tandem repeat in the genome, and advances in next generation sequencing(NGS) technology have enabled <i>in silico</i> anlysis of full-length whole genome sequences. In this paper, we analyzed unknown samples provided by Robert Koch Institute(RKI) through The United Nation

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Trost, Brett, Susan Walker, Syed A. Haider, et al. "Impact of DNA source on genetic variant detection from human whole-genome sequencing data." Journal of Medical Genetics 56, no. 12 (2019): 809–17. http://dx.doi.org/10.1136/jmedgenet-2019-106281.

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BackgroundWhole blood is currently the most common DNA source for whole-genome sequencing (WGS), but for studies requiring non-invasive collection, self-collection, greater sample stability or additional tissue references, saliva or buccal samples may be preferred. However, the relative quality of sequencing data and accuracy of genetic variant detection from blood-derived, saliva-derived and buccal-derived DNA need to be thoroughly investigated.MethodsMatched blood, saliva and buccal samples from four unrelated individuals were used to compare sequencing metrics and variant-detection accuracy

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Au, Kin Fai, Jason G. Underwood, Lawrence Lee, and Wing Hung Wong. "Improving PacBio Long Read Accuracy by Short Read Alignment." PLoS ONE 7, no. 10 (2012): e46679. http://dx.doi.org/10.1371/journal.pone.0046679.

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Rajasagi, Mohini, Sachet A. Shukla, Edward F. Fritsch, et al. "Tumor Neoantigens Are Abundant Across Cancers." Blood 122, no. 21 (2013): 3265. http://dx.doi.org/10.1182/blood.v122.21.3265.3265.

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Abstract Tumor neoantigens are a promising class of vaccine immunogens as they arise from gene alterations in tumor cells and are hence exquisitely tumor-specific. We recently reported the development of a pipeline that leverages massively parallel sequencing data with HLA-peptide binding predictions to identify candidate neoantigens. By applying this pipeline to cases of chronic lymphocytic leukemia (CLL) with known HLA typing, we described the prediction of personal tumor neoantigens against which long-lived memory T cell responses developed following remission-inducing therapy. Our pipeline

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Gnerre, Sante, Brian Yik Tak Tsui, Tingting Jiang, et al. "Abstract 1220: Accurately genotyping HLA and KIR alleles using cfDNA assay and k-mer based algorithm for immunotherapy." Cancer Research 82, no. 12_Supplement (2022): 1220. http://dx.doi.org/10.1158/1538-7445.am2022-1220.

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Abstract Background: HLA and KIR genotypes show great promise as emerging biomarkers for immune checkpoint inhibitors (ICIs) and understanding patient prognosis. Multiple studies have shown that HLA-I heterozygosity and high sequence divergence across alleles positively correlates with response to ICIs. However the high degree of polymorphism and allele sequence similarities in HLA and KIR present a challenge to accurate allele calling. To address these difficulties we developed kmerizer, a novel allele caller optimized for short fragments, such as reads from a cfDNA assay. Methods: We tested

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Wilton, Richard, and Alexander S. Szalay. "Performance optimization in DNA short-read alignment." Bioinformatics 38, no. 8 (2022): 2081–87. http://dx.doi.org/10.1093/bioinformatics/btac066.

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Abstract Summary Over the past decade, short-read sequence alignment has become a mature technology. Optimized algorithms, careful software engineering and high-speed hardware have contributed to greatly increased throughput and accuracy. With these improvements, many opportunities for performance optimization have emerged. In this review, we examine three general-purpose short-read alignment tools—BWA-MEM, Bowtie 2 and Arioc—with a focus on performance optimization. We analyze the performance-related behavior of the algorithms and heuristics each tool implements, with the goal of arriving at

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Mahato, Rekha, Prem Chand Gyani, Akash Maity, et al. "Unlocking the Potential of Nanopore Sequencing: Principles, Advances, and Challenges." Journal of Biochemistry International 12, no. 1 (2025): 125–38. https://doi.org/10.56557/jobi/2025/v12i19267.

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DNA sequencing is nowadays considered as the most effective technique for detecting genetic differences among populations of a species at the molecular level. There are 3 (Three) generations of sequencing available, which can be efficiently utilized to determine genetic variations. Among all the generations of DNA sequencing, nanopore sequencing technology is anticipated to attain all the standard goals of molecular biology. Deamer, Branton, and coworkers in 1961 first demonstrated the DNA translocation using the α-hemolysin nanopore. In 2014, Oxford Nanopore Technologies' (ONT) MinION sequenc

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Nakabayashi, Ryo, and Shinichi Morishita. "HiC-Hiker: a probabilistic model to determine contig orientation in chromosome-length scaffolds with Hi-C." Bioinformatics 36, no. 13 (2020): 3966–74. http://dx.doi.org/10.1093/bioinformatics/btaa288.

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Abstract Motivation De novo assembly of reference-quality genomes used to require enormously laborious tasks. In particular, it is extremely time-consuming to build genome markers for ordering assembled contigs along chromosomes; thus, they are only available for well-established model organisms. To resolve this issue, recent studies demonstrated that Hi-C could be a powerful and cost-effective means to output chromosome-length scaffolds for non-model species with no genome marker resources, because the Hi-C contact frequency between a pair of two loci can be a good estimator of their genomic

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Rifqi, Meidianto, and Crestofel Lantu Donald. "Assessment of PT. XYZ's Change Management Initiatives towards Employee Readiness in Organization Restructuring." International Journal of Current Science Research and Review 06, no. 02 (2023): 1804–15. https://doi.org/10.5281/zenodo.7685616.

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<strong>ABSTRACT: </strong>Digital content and influencer marketing leader PT. XYZ Located at the crossroads of content, platforms, and brands, aims to revolutionize content creation, distribution, and consumption in Asia. Singapore, Kuala Lumpur, Seoul, Tokyo, Manila, Shenzhen, Hong Kong, and Jakarta are the 8 Asia Pacific offices (including Philippine after the merger with Indonesia). Organizational reorganization is essential, according to PT. XYZ. After Q1–Q3 2021 revenue declines, this campaign was launched. Employee readiness to adopt the new organizational structure must be assess

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Guguchkin, Egor Pavlovich, and Evgeny Andreevich Karpulevich. "Modification of the short read alignment algorithm to improve the quality of the human whole genome sequencing data processing pipeline." Proceedings of the Institute for System Programming of the RAS 35, no. 2 (2023): 235–48. http://dx.doi.org/10.15514/ispras-2023-35(2)-17.

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This study emphasizes the importance of aligning short reads in the analysis of human whole-genome sequencing data. The alignment process involves determining the positions of short genetic sequences relative to a known reference genome sequence of the human genome. Traditional alignment methods use a linear reference sequence, but this can lead to incorrect alignment, especially when short reads contain genetic variations. In this work, the index file of the reference sequence was modified using the minimap2 tool. Experimental results showed that adding information about frequently occurring

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Ji, Mingeun, Yejin Kan, Dongyeon Kim, Jaehee Jung, and Gangman Yi. "cPlot: Contig-Plotting Visualization for the Analysis of Short-Read Nucleotide Sequence Alignments." International Journal of Molecular Sciences 23, no. 19 (2022): 11484. http://dx.doi.org/10.3390/ijms231911484.

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Advances in the next-generation sequencing technology have led to a dramatic decrease in read-generation cost and an increase in read output. Reconstruction of short DNA sequence reads generated by next-generation sequencing requires a read alignment method that reconstructs a reference genome. In addition, it is essential to analyze the results of read alignments for a biologically meaningful inference. However, read alignment from vast amounts of genomic data from various organisms is challenging in that it involves repeated automatic and manual analysis steps. We, here, devised cPlot softwa

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Quan, Wei, Bo Liu, and Yadong Wang. "Fast and SNP-aware short read alignment with SALT." BMC Bioinformatics 22, S9 (2021). http://dx.doi.org/10.1186/s12859-021-04088-6.

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Abstract Background DNA sequence alignment is a common first step in most applications of high-throughput sequencing technologies. The accuracy of sequence alignments directly affects the accuracy of downstream analyses, such as variant calling and quantitative analysis of transcriptome; therefore, rapidly and accurately mapping reads to a reference genome is a significant topic in bioinformatics. Conventional DNA read aligners map reads to a linear reference genome (such as the GRCh38 primary assembly). However, such a linear reference genome represents the genome of only one or a few individ

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Blanke, Matthias, and Burkhard Morgenstern. "App-SpaM: Phylogenetic placement of short reads without sequence alignment." Bioinformatics Advances, October 13, 2021. http://dx.doi.org/10.1093/bioadv/vbab027.

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Abstract Motivation Phylogenetic placement is the task of placing a query sequence of unknown taxonomic origin into a given phylogenetic tree of a set of reference sequences. A major field of application of such methods is, for example, the taxonomic identification of reads in metabarcoding or metagenomic studies. Several approaches to phylogenetic placement have been proposed in recent years. The most accurate of them require a multiple sequence alignment of the references as input. However, calculating multiple alignments is not only time consuming, but also limits the applicability of these

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"NGS Short Read Alignment Algorithms and the role of Big Data and Cloud Computing." International Journal of Innovative Technology and Exploring Engineering 8, no. 9 (2019): 967–71. http://dx.doi.org/10.35940/ijitee.i8001.078919.

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Next Generation Sequencing (NGS) raises opportunities to the computational field for fast and accurate methods for the various challenges associated with NGS data. NGS technology generates a large set of short reads of size 50 to 400 base pairs as a result of biological experiments done on the samples taken from species. Such raw reads are not directly ready for doing most of the analysis or comparative studies to figure out medical related solutions. Hence, the reads have to be assembled to form a complete genome sequence. During the assembly process, there is a high chance of erroneous posit

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Ma, Jun, Manuel Cáceres, Leena Salmela, Veli Mäkinen, and Alexandru I. Tomescu. "Chaining for Accurate Alignment of Erroneous Long Reads to Acyclic Variation Graphs." Bioinformatics, July 26, 2023. http://dx.doi.org/10.1093/bioinformatics/btad460.

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Abstract Motivation Aligning reads to a variation graph is a standard task in pangenomics, with downstream applications such as improving variant calling. While the vg toolkit (Garrison et al., 2018) is a popular aligner of short reads, GraphAligner (Rautiainen and Marschall, 2020) is the state-of-the-art aligner of erroneous long reads. GraphAligner works by finding candidate read occurrences based on individually extending the best seeds of the read in the variation graph. However, a more principled approach recognized in the community is to co-linearly chain multiple seeds. Results We prese

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Varki, Rahul, Massimiliano Rossi, Eddie Ferro, et al. "Accurate short-read alignment throughr-index-based pangenome indexing." Genome Research, June 12, 2025. https://doi.org/10.1101/gr.279858.124.

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Aligning to a linear reference genome can result in a higher percentage of reads going unmapped or being incorrectly mapped owing to variations not captured by the reference, otherwise known as reference bias. Recently, in efforts to mitigate reference bias, there has been a movement to switch to using pangenomes, a collection of genomes, as the reference. In this paper, we introduce Moni-align, the first short-read pangenome aligner built on ther-index, a variation of the classical FM-index that can index collections of genomes in O(r)-space, whereris the number of runs in the Burrows–Wheeler

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Abou Saada, Omar, Andreas Tsouris, Chris Eberlein, Anne Friedrich, and Joseph Schacherer. "nPhase: an accurate and contiguous phasing method for polyploids." Genome Biology 22, no. 1 (2021). http://dx.doi.org/10.1186/s13059-021-02342-x.

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AbstractWhile genome sequencing and assembly are now routine, we do not have a full, precise picture of polyploid genomes. No existing polyploid phasing method provides accurate and contiguous haplotype predictions. We developed nPhase, a ploidy agnostic tool that leverages long reads and accurate short reads to solve alignment-based phasing for samples of unspecified ploidy (https://github.com/OmarOakheart/nPhase). nPhase is validated by tests on simulated and real polyploids. nPhase obtains on average over 95% accuracy and a contiguous 1.25 haplotigs per haplotype to cover more than 90% of e

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Luo, Junwei, Runtian Gao, Wenjing Chang, and Junfeng Wang. "LSnet: detecting and genotyping deletions using deep learning network." Frontiers in Genetics 14 (June 14, 2023). http://dx.doi.org/10.3389/fgene.2023.1189775.

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The role and biological impact of structural variation (SV) are increasingly evident. Deletion accounts for 40% of SV and is an important type of SV. Therefore, it is of great significance to detect and genotype deletions. At present, high accurate long reads can be obtained as HiFi reads. And, through a combination of error-prone long reads and high accurate short reads, we can also get accurate long reads. These accurate long reads are helpful for detecting and genotyping SVs. However, due to the complexity of genome and alignment information, detecting and genotyping SVs remain a challengin

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