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Journal articles on the topic 'Short Read Mapping (SRM)'

Author: Grafiati

Published: 6 September 2023

Last updated: 31 July 2025

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1

Chon, Alvin, and Xiaoqiu Huang. "SRAMM: Short Read Alignment Mapping Metrics." International Journal on Bioinformatics & Biosciences 11, no. 02 (2021): 01–07. http://dx.doi.org/10.5121/ijbb.2021.11201.

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Short Read Alignment Mapping Metrics (SRAMM): is an efficient and versatile command line tool providing additional short read mapping metrics, filtering, and graphs. Short read aligners report MAPing Quality (MAPQ), but these methods generally are neither standardized nor well described in literature or software manuals. Additionally, third party mapping quality programs are typically computationally intensive or designed for specific applications. SRAMM efficiently generates multiple different concept-based mapping scores to provide for an informative post alignment examination and filtering

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2

Cline, Eliot, Nuttachat Wisittipanit, Tossapon Boongoen, Ekachai Chukeatirote, Darush Struss, and Anant Eungwanichayapant. "Recalibration of mapping quality scores in Illumina short-read alignments improves SNP detection results in low-coverage sequencing data." PeerJ 8 (December 7, 2020): e10501. http://dx.doi.org/10.7717/peerj.10501.

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Background Low-coverage sequencing is a cost-effective way to obtain reads spanning an entire genome. However, read depth at each locus is low, making sequencing error difficult to separate from actual variation. Prior to variant calling, sequencer reads are aligned to a reference genome, with alignments stored in Sequence Alignment/Map (SAM) files. Each alignment has a mapping quality (MAPQ) score indicating the probability a read is incorrectly aligned. This study investigated the recalibration of probability estimates used to compute MAPQ scores for improving variant calling performance in

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3

Yang, Xiaohong, Yue Li, Yu Wei, Zhanlong Chen, and Peng Xie. "Water Body Extraction from Sentinel-3 Image with Multiscale Spatiotemporal Super-Resolution Mapping." Water 12, no. 9 (2020): 2605. http://dx.doi.org/10.3390/w12092605.

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Water body mapping is significant for water resource management. In the view of 21 spectral bands and a short revisit time of no more than two days, a Sentinel-3 OLCI (Ocean and Land Colour Instrument) image could be the optimum data source in the near-real-time mapping of water bodies. However, the image is often limited by its low spatial resolution in practice. Super-resolution mapping (SRM) is a good solution to generate finer spatial resolution maps than the input data allows. In this paper, a multiscale spatiotemporal super-resolution mapping (MSST_SRM) method for water bodies is propose

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4

Alvin, Chon. "SRAMM: SHORT READ ALIGNMENT MAPPING METRICS." International Journal on Bioinformatics & Biosciences (IJBB) Vol 11, No.1/2, June 2021 11, June (2021): 1–7. https://doi.org/10.5281/zenodo.5084755.

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Short Read Alignment Mapping Metrics (SRAMM): is an efficient and versatile command line tool providing additional short read mapping metrics, filtering, and graphs. Short read aligners report MAPing Quality (MAPQ), but these methods generally are neither standardized nor well described in literature or software manuals. Additionally, third party mapping quality programs are typically computationally intensive or designed for specific applications. SRAMM efficiently generates multiple different concept-based mapping scores to provide for an informative post alignment examination and filtering

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Canzar, Stefan, and Steven L. Salzberg. "Short Read Mapping: An Algorithmic Tour." Proceedings of the IEEE 105, no. 3 (2017): 436–58. http://dx.doi.org/10.1109/jproc.2015.2455551.

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6

Deorowicz, Sebastian, and Adam Gudyś. "Whisper 2: Indel-sensitive short read mapping." SoftwareX 14 (June 2021): 100692. http://dx.doi.org/10.1016/j.softx.2021.100692.

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7

David, Matei, Misko Dzamba, Dan Lister, Lucian Ilie, and Michael Brudno. "SHRiMP2: Sensitive yet Practical Short Read Mapping." Bioinformatics 27, no. 7 (2011): 1011–12. http://dx.doi.org/10.1093/bioinformatics/btr046.

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8

Smith, A. D., W. Y. Chung, E. Hodges, et al. "Updates to the RMAP short-read mapping software." Bioinformatics 25, no. 21 (2009): 2841–42. http://dx.doi.org/10.1093/bioinformatics/btp533.

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9

Tran, Hong, Jacob Porter, Ming-an Sun, Hehuang Xie, and Liqing Zhang. "Objective and Comprehensive Evaluation of Bisulfite Short Read Mapping Tools." Advances in Bioinformatics 2014 (April 15, 2014): 1–11. http://dx.doi.org/10.1155/2014/472045.

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Background. Large-scale bisulfite treatment and short reads sequencing technology allow comprehensive estimation of methylation states of Cs in the genomes of different tissues, cell types, and developmental stages. Accurate characterization of DNA methylation is essential for understanding genotype phenotype association, gene and environment interaction, diseases, and cancer. Aligning bisulfite short reads to a reference genome has been a challenging task. We compared five bisulfite short read mapping tools, BSMAP, Bismark, BS-Seeker, BiSS, and BRAT-BW, representing two classes of mapping alg

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10

Gao, Lei, Cong Wu, and Lin Liu. "AUSPP: A universal short-read pre-processing package." Journal of Bioinformatics and Computational Biology 17, no. 06 (2019): 1950037. http://dx.doi.org/10.1142/s0219720019500379.

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There are many short-read aligners that can map short reads to a reference genome/sequence, and most of them can directly accept a FASTQ file as the input query file. However, the raw data usually need to be pre-processed. Few software programs specialize in pre-processing raw data generated by a variety of next-generation sequencing (NGS) technologies. Here, we present AUSPP, a Perl script-based pipeline for pre-processing and automatic mapping of NGS short reads. This pipeline encompasses quality control, adaptor trimming, collapsing of reads, structural RNA removal, length selection, read m

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11

Hach, Faraz, Fereydoun Hormozdiari, Can Alkan, et al. "mrsFAST: a cache-oblivious algorithm for short-read mapping." Nature Methods 7, no. 8 (2010): 576–77. http://dx.doi.org/10.1038/nmeth0810-576.

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12

Martinez, Hector, Joaquin Tarraga, Ignacio Medina, et al. "Concurrent and Accurate Short Read Mapping on Multicore Processors." IEEE/ACM Transactions on Computational Biology and Bioinformatics 12, no. 5 (2015): 995–1007. http://dx.doi.org/10.1109/tcbb.2015.2392077.

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13

Houtgast, Ernst Joachim, Vlad-Mihai Sima, Koen Bertels, and Zaid Al-Ars. "Hardware acceleration of BWA-MEM genomic short read mapping for longer read lengths." Computational Biology and Chemistry 75 (August 2018): 54–64. http://dx.doi.org/10.1016/j.compbiolchem.2018.03.024.

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14

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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15

Linheiro, Raquel, and John Archer. "Quantification of the effects of chimerism on read mapping, differential expression and annotation following short-read de novo assembly." F1000Research 11 (January 31, 2022): 120. http://dx.doi.org/10.12688/f1000research.108489.1.

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Background: De novo assembly is often required for analysing short-read RNA sequencing data. An under-characterized aspect of the contigs produced is chimerism, the extent to which affects mapping, differential expression analysis and annotation. Despite long-read sequencing negating this issue, short-reads remain in use through on-going research and archived datasets created during the last two decades. Consequently, there is still a need to quantify chimerism and its effects. Methods: Effects on mapping were quantified by simulating reads off the Drosophila melanogaster cDNA library and mapp

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Tewolde, Rediat, Timothy Dallman, Ulf Schaefer, et al. "MOST: a modified MLST typing tool based on short read sequencing." PeerJ 4 (August 17, 2016): e2308. http://dx.doi.org/10.7717/peerj.2308.

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Multilocus sequence typing (MLST) is an effective method to describe bacterial populations. Conventionally, MLST involves Polymerase Chain Reaction (PCR) amplification of housekeeping genes followed by Sanger DNA sequencing. Public Health England (PHE) is in the process of replacing the conventional MLST methodology with a method based on short read sequence data derived from Whole Genome Sequencing (WGS). This paper reports the comparison of the reliability of MLST results derived from WGS data, comparing mapping and assembly-based approaches to conventional methods using 323 bacterial genome

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17

Wood, David L. A., Qinying Xu, John V. Pearson, Nicole Cloonan, and Sean M. Grimmond. "X-MATE: a flexible system for mapping short read data." Bioinformatics 27, no. 4 (2011): 580–81. http://dx.doi.org/10.1093/bioinformatics/btq698.

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Pireddu, L., S. Leo, and G. Zanetti. "SEAL: a distributed short read mapping and duplicate removal tool." Bioinformatics 27, no. 15 (2011): 2159–60. http://dx.doi.org/10.1093/bioinformatics/btr325.

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19

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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20

Cechova, Monika. "Probably Correct: Rescuing Repeats with Short and Long Reads." Genes 12, no. 1 (2020): 48. http://dx.doi.org/10.3390/genes12010048.

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Ever since the introduction of high-throughput sequencing following the human genome project, assembling short reads into a reference of sufficient quality posed a significant problem as a large portion of the human genome—estimated 50–69%—is repetitive. As a result, a sizable proportion of sequencing reads is multi-mapping, i.e., without a unique placement in the genome. The two key parameters for whether or not a read is multi-mapping are the read length and genome complexity. Long reads are now able to span difficult, heterochromatic regions, including full centromeres, and characterize chr

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21

Peng, Mengfei, Morgan L. Davis, Meghan L. Bentz, et al. "Short-Read and Long-Read Whole Genome Sequencing for SARS-CoV-2 Variants Identification." Viruses 17, no. 4 (2025): 584. https://doi.org/10.3390/v17040584.

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Genomic surveillance of SARS-CoV-2 is crucial for detecting emerging variants and informing public health responses. Various sequencing technologies are used for whole genome sequencing of SARS-CoV-2. This cross-platform benchmark study applied established bioinformatics tools to assess and improve the performance of Illumina NovaSeq, Oxford Nanopore Technologies MinION, and Pacific Biosciences Sequel II sequencing platforms in identifying SARS-CoV-2 variants and lineage assignment. NovaSeq produced the highest number of reads and bases, depth of coverage, completeness of consensus genomes, st

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22

Budurlean, Laura, Diwakar Bastihalli Tukaramrao, Lijun Zhang, Sinisa Dovat, and James Broach. "Integrating Optical Genome Mapping and Whole Genome Sequencing in Somatic Structural Variant Detection." Journal of Personalized Medicine 14, no. 3 (2024): 291. http://dx.doi.org/10.3390/jpm14030291.

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Structural variants drive tumorigenesis by disrupting normal gene function through insertions, inversions, translocations, and copy number changes, including deletions and duplications. Detecting structural variants is crucial for revealing their roles in tumor development, clinical outcomes, and personalized therapy. Presently, most studies rely on short-read data from next-generation sequencing that aligns back to a reference genome to determine if and, if so, where a structural variant occurs. However, structural variant discovery by short-read sequencing is challenging, primarily because o

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23

Wong, Kwong-Kwok, Yvonne Tsang, and David M. Gershenson. "Abstract 4081: Analysis of low-grade serous ovarian cancer by long-read full length transcripts sequencing." Cancer Research 85, no. 8_Supplement_1 (2025): 4081. https://doi.org/10.1158/1538-7445.am2025-4081.

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Abstract Low grade serous ovarian carcinoma is a rare epithelial ovarian cancer that occurs more frequently in younger women. RNA sequencing (RNAseq) has been playing a pivotal role in understanding the molecular pathogenesis of the low-grade ovarian serous carcinoma (LGSOC). The quantification of gene expression with enough sequencing depth can be fairly accurate. However, the current short-read RNAseq approach is not very accurate in measuring individual transcript activity. This is because multiple transcripts from the same gene share high sequence similarity, which complicates the transcri

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Houtgast, Ernst Joachim, VladMihai Sima, Koen Bertels, and Zaid AlArs. "An Efficient GPUAccelerated Implementation of Genomic Short Read Mapping with BWAMEM." ACM SIGARCH Computer Architecture News 44, no. 4 (2017): 38–43. http://dx.doi.org/10.1145/3039902.3039910.

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25

Porter, Jacob, Ming-an Sun, Hehuang Xie, and Liqing Zhang. "Investigating bisulfite short-read mapping failure with hairpin bisulfite sequencing data." BMC Genomics 16, Suppl 11 (2015): S2. http://dx.doi.org/10.1186/1471-2164-16-s11-s2.

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26

Guo, Lilu, and Hongwei Huo. "An efficient Burrows–Wheeler transform-based aligner for short read mapping." Computational Biology and Chemistry 110 (June 2024): 108050. http://dx.doi.org/10.1016/j.compbiolchem.2024.108050.

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27

Gouil, Quentin, and Andrew Keniry. "Latest techniques to study DNA methylation." Essays in Biochemistry 63, no. 6 (2019): 639–48. http://dx.doi.org/10.1042/ebc20190027.

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Abstract Bisulfite sequencing is a powerful technique to detect 5-methylcytosine in DNA that has immensely contributed to our understanding of epigenetic regulation in plants and animals. Meanwhile, research on other base modifications, including 6-methyladenine and 4-methylcytosine that are frequent in prokaryotes, has been impeded by the lack of a comparable technique. Bisulfite sequencing also suffers from a number of drawbacks that are difficult to surmount, among which DNA degradation, lack of specificity, or short reads with low sequence diversity. In this review, we explore the recent r

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Limasset, Antoine, Jean-François Flot, and Pierre Peterlongo. "Toward perfect reads: self-correction of short reads via mapping on de Bruijn graphs." Bioinformatics 36, no. 5 (2019): 1374–81. http://dx.doi.org/10.1093/bioinformatics/btz102.

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Abstract Motivation Short-read accuracy is important for downstream analyses such as genome assembly and hybrid long-read correction. Despite much work on short-read correction, present-day correctors either do not scale well on large datasets or consider reads as mere suites of k-mers, without taking into account their full-length sequence information. Results We propose a new method to correct short reads using de Bruijn graphs and implement it as a tool called Bcool. As a first step, Bcool constructs a compacted de Bruijn graph from the reads. This graph is filtered on the basis of k-mer ab

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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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Kainth, Amoldeep S., Gabriela A. Haddad, Johnathon M. Hall, and Alexander J. Ruthenburg. "Merging short and stranded long reads improves transcript assembly." PLOS Computational Biology 19, no. 10 (2023): e1011576. http://dx.doi.org/10.1371/journal.pcbi.1011576.

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Long-read RNA sequencing has arisen as a counterpart to short-read sequencing, with the potential to capture full-length isoforms, albeit at the cost of lower depth. Yet this potential is not fully realized due to inherent limitations of current long-read assembly methods and underdeveloped approaches to integrate short-read data. Here, we critically compare the existing methods and develop a new integrative approach to characterize a particularly challenging pool of low-abundance long noncoding RNA (lncRNA) transcripts from short- and long-read sequencing in two distinct cell lines. Our analy

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Castells-Rufas, David, Santiago Marco-Sola, Juan Carlos Moure, Quim Aguado, and Antonio Espinosa. "FPGA Acceleration of Pre-Alignment Filters for Short Read Mapping With HLS." IEEE Access 10 (2022): 22079–100. http://dx.doi.org/10.1109/access.2022.3153032.

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Pandey, Ram Vinay, and Christian Schlötterer. "DistMap: A Toolkit for Distributed Short Read Mapping on a Hadoop Cluster." PLoS ONE 8, no. 8 (2013): e72614. http://dx.doi.org/10.1371/journal.pone.0072614.

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33

Ruffalo, M., M. Koyuturk, S. Ray, and T. LaFramboise. "Accurate estimation of short read mapping quality for next-generation genome sequencing." Bioinformatics 28, no. 18 (2012): i349—i355. http://dx.doi.org/10.1093/bioinformatics/bts408.

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34

Southgate, Joel A., Matthew J. Bull, Clare M. Brown, et al. "Influenza classification from short reads with VAPOR facilitates robust mapping pipelines and zoonotic strain detection for routine surveillance applications." Bioinformatics 36, no. 6 (2019): 1681–88. http://dx.doi.org/10.1093/bioinformatics/btz814.

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Abstract Motivation Influenza viruses represent a global public health burden due to annual epidemics and pandemic potential. Due to a rapidly evolving RNA genome, inter-species transmission, intra-host variation, and noise in short-read data, reads can be lost during mapping, and de novo assembly can be time consuming and result in misassembly. We assessed read loss during mapping and designed a graph-based classifier, VAPOR, for selecting mapping references, assembly validation and detection of strains of non-human origin. Results Standard human reference viruses were insufficient for mappin

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Richmond, Phillip Andrew, Alice Mary Kaye, Godfrain Jacques Kounkou, Tamar Vered Av-Shalom, and Wyeth W. Wasserman. "Demonstrating the utility of flexible sequence queries against indexed short reads with FlexTyper." PLOS Computational Biology 17, no. 3 (2021): e1008815. http://dx.doi.org/10.1371/journal.pcbi.1008815.

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Across the life sciences, processing next generation sequencing data commonly relies upon a computationally expensive process where reads are mapped onto a reference sequence. Prior to such processing, however, there is a vast amount of information that can be ascertained from the reads, potentially obviating the need for processing, or allowing optimized mapping approaches to be deployed. Here, we present a method termed FlexTyper which facilitates a “reverse mapping” approach in which high throughput sequence queries, in the form of k-mer searches, are run against indexed short-read datasets

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Lee, Wan-Ping, Michael P. Stromberg, Alistair Ward, Chip Stewart, Erik P. Garrison, and Gabor T. Marth. "MOSAIK: A Hash-Based Algorithm for Accurate Next-Generation Sequencing Short-Read Mapping." PLoS ONE 9, no. 3 (2014): e90581. http://dx.doi.org/10.1371/journal.pone.0090581.

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37

Wei, Po-Li, Ching-Sheng Hung, Yi-Wei Kao, et al. "Characterization of Fecal Microbiota with Clinical Specimen Using Long-Read and Short-Read Sequencing Platform." International Journal of Molecular Sciences 21, no. 19 (2020): 7110. http://dx.doi.org/10.3390/ijms21197110.

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Accurate and rapid identification of microbiotic communities using 16S ribosomal (r)RNA sequencing is a critical task for expanding medical and clinical applications. Next-generation sequencing (NGS) is widely considered a practical approach for direct application to communities without the need for in vitro culturing. In this report, a comparative evaluation of short-read (Illumina) and long-read (Oxford Nanopore Technologies (ONT)) platforms toward 16S rRNA sequencing with the same batch of total genomic DNA extracted from fecal samples is presented. Different 16S gene regions were amplified

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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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Kim, Youngho, Munseong Kang, Ju-Hui Jeong, Dae Woong Kang, Soo Jun Park, and Jeong Seop Sim. "Reference Mapping Considering Swaps of Adjacent Bases." Applied Sciences 11, no. 11 (2021): 5038. http://dx.doi.org/10.3390/app11115038.

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Since the time of the HGP, research into next-generation sequencing, which can reduce the cost and time of sequence analysis using computer algorithms, has been actively conducted. Mapping is a next-generation sequencing method that identifies sequences by aligning short reads with a reference genome for which sequence information is known. Mapping can be applied to tasks such as SNP calling, motif searches, and gene identification. Research on mapping that utilizes BWT and GPU has been undertaken in order to obtain faster mapping. In this paper, we propose a new mapping algorithm with additio

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Soto, Daniela C., Colin Shew, Mira Mastoras, et al. "Identification of Structural Variation in Chimpanzees Using Optical Mapping and Nanopore Sequencing." Genes 11, no. 3 (2020): 276. http://dx.doi.org/10.3390/genes11030276.

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Recent efforts to comprehensively characterize great ape genetic diversity using short-read sequencing and single-nucleotide variants have led to important discoveries related to selection within species, demographic history, and lineage-specific traits. Structural variants (SVs), including deletions and inversions, comprise a larger proportion of genetic differences between and within species, making them an important yet understudied source of trait divergence. Here, we used a combination of long-read and -range sequencing approaches to characterize the structural variant landscape of two ad

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Watson, Simon J., Matthijs R. A. Welkers, Daniel P. Depledge, et al. "Viral population analysis and minority-variant detection using short read next-generation sequencing." Philosophical Transactions of the Royal Society B: Biological Sciences 368, no. 1614 (2013): 20120205. http://dx.doi.org/10.1098/rstb.2012.0205.

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RNA viruses within infected individuals exist as a population of evolutionary-related variants. Owing to evolutionary change affecting the constitution of this population, the frequency and/or occurrence of individual viral variants can show marked or subtle fluctuations. Since the development of massively parallel sequencing platforms, such viral populations can now be investigated to unprecedented resolution. A critical problem with such analyses is the presence of sequencing-related errors that obscure the identification of true biological variants present at low frequency. Here, we report

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Valiente-Mullor, Carlos, Beatriz Beamud, Iván Ansari, et al. "One is not enough: On the effects of reference genome for the mapping and subsequent analyses of short-reads." PLOS Computational Biology 17, no. 1 (2021): e1008678. http://dx.doi.org/10.1371/journal.pcbi.1008678.

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Mapping of high-throughput sequencing (HTS) reads to a single arbitrary reference genome is a frequently used approach in microbial genomics. However, the choice of a reference may represent a source of errors that may affect subsequent analyses such as the detection of single nucleotide polymorphisms (SNPs) and phylogenetic inference. In this work, we evaluated the effect of reference choice on short-read sequence data from five clinically and epidemiologically relevant bacteria (Klebsiella pneumoniae, Legionella pneumophila, Neisseria gonorrhoeae, Pseudomonas aeruginosa and Serratia marcesce

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Chen, Yen-Lung, Bo-Yi Chang, Chia-Hsiang Yang, and Tzi-Dar Chiueh. "A High-Throughput FPGA Accelerator for Short-Read Mapping of the Whole Human Genome." IEEE Transactions on Parallel and Distributed Systems 32, no. 6 (2021): 1465–78. http://dx.doi.org/10.1109/tpds.2021.3051011.

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Zhao, Qiong-Yi, Jacob Gratten, Restuadi Restuadi, and Xuan Li. "Mapping and differential expression analysis from short-read RNA-Seq data in model organisms." Quantitative Biology 4, no. 1 (2016): 22–35. http://dx.doi.org/10.1007/s40484-016-0060-7.

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Alser, Mohammed, Hasan Hassan, Hongyi Xin, Oğuz Ergin, Onur Mutlu, and Can Alkan. "GateKeeper: a new hardware architecture for accelerating pre-alignment in DNA short read mapping." Bioinformatics 33, no. 21 (2017): 3355–63. http://dx.doi.org/10.1093/bioinformatics/btx342.

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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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Feng, Yi, Leslie Y. Beh, Wei-Jen Chang, and Laura F. Landweber. "SIGAR: Inferring Features of Genome Architecture and DNA Rearrangements by Split-Read Mapping." Genome Biology and Evolution 12, no. 10 (2020): 1711–18. http://dx.doi.org/10.1093/gbe/evaa147.

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Abstract Ciliates are microbial eukaryotes with distinct somatic and germline genomes. Postzygotic development involves extensive remodeling of the germline genome to form somatic chromosomes. Ciliates therefore offer a valuable model for studying the architecture and evolution of programed genome rearrangements. Current studies usually focus on a few model species, where rearrangement features are annotated by aligning reference germline and somatic genomes. Although many high-quality somatic genomes have been assembled, a high-quality germline genome assembly is difficult to obtain due to it

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Weissensteiner, Matthias H., Andy W. C. Pang, Ignas Bunikis, et al. "Combination of short-read, long-read, and optical mapping assemblies reveals large-scale tandem repeat arrays with population genetic implications." Genome Research 27, no. 5 (2017): 697–708. http://dx.doi.org/10.1101/gr.215095.116.

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Jeske, Tim, Peter Huypens, Laura Stirm, et al. "DEUS: an R package for accurate small RNA profiling based on differential expression of unique sequences." Bioinformatics 35, no. 22 (2019): 4834–36. http://dx.doi.org/10.1093/bioinformatics/btz495.

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Abstract Summary Despite their fundamental role in various biological processes, the analysis of small RNA sequencing data remains a challenging task. Major obstacles arise when short RNA sequences map to multiple locations in the genome, align to regions that are not annotated or underwent post-transcriptional changes which hamper accurate mapping. In order to tackle these issues, we present a novel profiling strategy that circumvents the need for read mapping to a reference genome by utilizing the actual read sequences to determine expression intensities. After differential expression analys

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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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