Literature DB >> 21154709

Aligning short sequencing reads with Bowtie.

Ben Langmead1.   

Abstract

This unit shows how to use the Bowtie package to align short sequencing reads, such as those output by second-generation sequencing instruments. It also includes protocols for building a genome index and calling consensus sequences from Bowtie alignments using SAMtools.

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Mesh：

Year:  2010        PMID： 21154709      PMCID： PMC3010897          DOI： 10.1002/0471250953.bi1107s32

Source DB:  PubMed          Journal:  Curr Protoc Bioinformatics        ISSN： 1934-3396


  2 in total

1.  The Sequence Alignment/Map format and SAMtools.

Authors:  Heng Li; Bob Handsaker; Alec Wysoker; Tim Fennell; Jue Ruan; Nils Homer; Gabor Marth; Goncalo Abecasis; Richard Durbin
Journal:  Bioinformatics       Date:  2009-06-08       Impact factor: 6.937

2.  Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.

Authors:  Ben Langmead; Cole Trapnell; Mihai Pop; Steven L Salzberg
Journal:  Genome Biol       Date:  2009-03-04       Impact factor: 13.583
  2 in total
  467 in total

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2.  BreakDancer: Identification of Genomic Structural Variation from Paired-End Read Mapping.

Authors:  Xian Fan; Travis E Abbott; David Larson; Ken Chen
Journal:  Curr Protoc Bioinformatics       Date:  2014

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Journal:  Mol Genet Genomics       Date:  2015-02-28       Impact factor: 3.291

4.  miRSwitch: detecting microRNA arm shift and switch events.

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Journal:  Nucleic Acids Res       Date:  2020-07-02       Impact factor: 16.971

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Authors:  Simon L Currie; Jedediah J Doane; Kathryn S Evans; Niraja Bhachech; Bethany J Madison; Desmond K W Lau; Lawrence P McIntosh; Jack J Skalicky; Kathleen A Clark; Barbara J Graves
Journal:  J Mol Biol       Date:  2017-07-17       Impact factor: 5.469

6.  Transcriptome profiling of the cancer and normal tissues from gastric cancer patients by deep sequencing.

Authors:  Fei-Gong Zhang; Zhi-Ying He; Qiang Wang
Journal:  Tumour Biol       Date:  2014-04-30

7.  MetAMOS: a modular and open source metagenomic assembly and analysis pipeline.

Authors:  Todd J Treangen; Sergey Koren; Daniel D Sommer; Bo Liu; Irina Astrovskaya; Brian Ondov; Aaron E Darling; Adam M Phillippy; Mihai Pop
Journal:  Genome Biol       Date:  2013-01-15       Impact factor: 13.583

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Authors:  Yotaro Ochi; Ayana Kon; Toyonori Sakata; Masahiro M Nakagawa; Naotaka Nakazawa; Masanori Kakuta; Keisuke Kataoka; Haruhiko Koseki; Manabu Nakayama; Daisuke Morishita; Tatsuaki Tsuruyama; Ryunosuke Saiki; Akinori Yoda; Rurika Okuda; Tetsuichi Yoshizato; Kenichi Yoshida; Yusuke Shiozawa; Yasuhito Nannya; Shinichi Kotani; Yasunori Kogure; Nobuyuki Kakiuchi; Tomomi Nishimura; Hideki Makishima; Luca Malcovati; Akihiko Yokoyama; Kengo Takeuchi; Eiji Sugihara; Taka-Aki Sato; Masashi Sanada; Akifumi Takaori-Kondo; Mario Cazzola; Mineko Kengaku; Satoru Miyano; Katsuhiko Shirahige; Hiroshi I Suzuki; Seishi Ogawa
Journal:  Cancer Discov       Date:  2020-04-05       Impact factor: 39.397

10.  A significant fraction of 21-nucleotide small RNA originates from phased degradation of resistance genes in several perennial species.

Authors:  Thomas Källman; Jun Chen; Niclas Gyllenstrand; Ulf Lagercrantz
Journal:  Plant Physiol       Date:  2013-04-11       Impact factor: 8.340
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