1400:
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351:) to keep its memory footprint small. Due to its implementation, Bowtie 2 is more suited to finding longer, gapped alignments in comparison with the original Bowtie method. There is no upper limit on read length in Bowtie 2 and it allows alignments to overlap ambiguous characters in the reference.
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through the space of possible alignments. Because the search is greedy, the first valid alignment encountered by Bowtie will not necessarily be the 'best' in terms of the number of mismatches or in terms of quality.
1200:
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677:; Goff, Loyal; Pertea, Geo; Kim, Daehwan; Kelley, David R; Pimentel, Harold; Salzberg, Steven L; Rinn, John L; Pachter, Lior (1 March 2012).
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727:"CummeRbund - An R package for persistent storage, analysis, and visualization of RNA-Seq from cufflinks output"
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679:"Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks"
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Bowtie is used as a sequence aligner by a number of other related bioinformatics algorithms, including
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International
Conference on Computational Intelligence Methods for Bioinformatics and Biostatistics
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paper describing the original Bowtie method has been cited more than 11,000 times. Bowtie is
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304:(typically to around 2.2GB for the human genome); a similar method is used by the BWA and
8:
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Li, R.; Yu, C.; Li, Y.; Lam, T.-W.; Yiu, S.-M.; Kristiansen, K.; Wang, J. (3 June 2009).
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Microsoft
Research - University of Trento Centre for Computational and Systems Biology
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561:
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422:"Ultrafast and memory-efficient alignment of short DNA sequences to the human genome"
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292:. Bowtie is promoted as "an ultrafast, memory-efficient short aligner for short
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Langmead, Ben; Cole
Trapnell; Mihai Pop; Steven L Salzberg (4 March 2009).
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sequences." The speed increase of Bowtie is partly due to implementing the
274:
52:
30:
510:"Bowtie: An ultrafast, memory-efficient short read aligner - SourceForge"
145:
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Ferragina, Paolo; Manzini, Giovanni (2005). "Indexing compressed text".
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532:"Fast and accurate short read alignment with Burrows-Wheeler transform"
47:
25:
343:. In addition to the Burrows-Wheeler transform, Bowtie 2 also uses an
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in 2009. The aligner is typically used with short reads and a large
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African
Society for Bioinformatics and Computational Biology
581:"SOAP2: an improved ultrafast tool for short read alignment"
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Max Planck
Institute of Molecular Cell Biology and Genetics
906:
368:"Bowtie: An ultrafast, memory-efficient short read aligner"
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293:
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International
Nucleotide Sequence Database Collaboration
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The Bowtie sequence aligner was originally developed by
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Bowtie conducts a quality-aware, greedy, randomized,
626:"TopHat: discovering splice junctions with RNA-Seq"
335:On 16 October 2011, the developers released a beta
875:, database of protein sequences grouping together
747:Langmead, Ben; Salzberg, Steven L (4 March 2012).
235:. The source code for the package is distributed
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1110:US National Center for Biotechnology Information
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1262:ISCB Africa ASBCB Conference on Bioinformatics
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1209:Institute of Genomics and Integrative Biology
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392:"Bowtie 2: fast and sensitive read alignment"
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239:and compiled binaries are available for
223:is a software package commonly used for
16:Sequence alignment and analysis software
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1189:International Society for Biocuration
1087:European Molecular Biology Laboratory
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1454:Software using the Artistic license
1215:Japanese Society for Bioinformatics
624:; Salzberg, S. L. (16 March 2009).
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1177:European Molecular Biology network
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530:Li, H.; Durbin, R. (18 May 2009).
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1171:Australia Bioinformatics Resource
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1121:Netherlands Bioinformatics Centre
1081:European Bioinformatics Institute
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1069:Database Center for Life Science
1057:Computational Biology Department
945:Arabidopsis Information Resource
300:for aligning, which reduces the
915:Specialised genomic databases:
323:, Cufflinks and the CummeRbund
261:and is currently maintained by
1116:Japanese Institute of Genetics
384:
360:
1:
1036:Rosalind (education platform)
953:Zebrafish Information Network
921:Saccharomyces Genome Database
642:10.1093/bioinformatics/btp120
598:10.1093/bioinformatics/btp336
548:10.1093/bioinformatics/btp324
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1366:List of biological databases
885:Protein Information Resource
804:Bowtie 2 page on SourceForge
95:2.4.2 / October 5, 2020
7:
859:European Nucleotide Archive
330:
251:platforms. As of 2017, the
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799:Bowtie page on SourceForge
396:bowtie-bio.sourceforge.net
372:bowtie-bio.sourceforge.net
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77:1.3.0 / July 22, 2020
1439:Bioinformatics algorithms
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439:10.1186/gb-2009-10-3-r25
263:Johns Hopkins University
1444:Bioinformatics software
1371:Molecular phylogenetics
867:China National GeneBank
485:10.1145/1082036.1082039
1075:DNA Data Bank of Japan
863:DNA Data Bank of Japan
695:10.1038/nprot.2012.016
339:of the project called
282:University of Maryland
1356:Computational biology
871:Secondary databases:
290:whole genome analysis
97:; 3 years ago
79:; 4 years ago
853:Sequence databases:
308:alignment methods.
259:open-source software
1449:Laboratory software
1149:Whitehead Institute
937:Rat Genome Database
21:
1386:Sequence alignment
1093:Flatiron Institute
765:10.1038/nmeth.1923
473:Journal of the ACM
313:depth-first search
225:sequence alignment
26:Original author(s)
19:
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1381:Sequence database
895:Protein Data Bank
889:Other databases:
591:(15): 1966–1967.
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229:sequence analysis
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759:(4): 357–359.
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620:Trapnell, C.;
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585:Bioinformatics
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1310:Nexus format
1305:NeXML format
1300:FASTQ format
1295:FASTA format
1283:File formats
1045:Institutions
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349:suffix array
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325:Bioconductor
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275:Ben Langmead
272:
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220:
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210:.sourceforge
150:/BenLangmead
140:
134:/BenLangmead
124:
53:Ben Langmead
48:Developer(s)
31:Ben Langmead
1290:CRAM format
1211:(CSIR-IGIB)
622:Pachter, L.
515:29 November
208:.bowtie-bio
1433:Categories
1376:Sequencing
1340:GTF format
1335:GFF format
1330:VCF format
1320:SAM format
1083:(EMBL-EBI)
1009:SOAP suite
929:VectorBase
891:BioNumbers
877:Swiss-Prot
401:2021-03-28
377:2021-03-28
355:References
159:Written in
120:Repository
102:2020-10-05
84:2020-07-22
1203:(ISCB-SC)
1173:(EMBL-AR)
1106:(MPI-CBG)
847:Databases
732:11 August
327:package.
288:, or for
38:Mihai Pop
1405:Category
1275:(RECOMB)
1225:Meetings
1179:(EMBnet)
1029:Server:
1004:SAMtools
999:PANGOLIN
962:Software
941:PHI-base
933:WormBase
903:InterPro
783:22388286
713:22383036
660:19289445
607:19497933
566:19451168
458:19261174
345:FM-index
341:Bowtie 2
331:Bowtie 2
152:/bowtie2
141:Bowtie 2
92:Bowtie 2
1417:Commons
1252:(InCoB)
1197:(ISCB)
1185:(INSDC)
1167:(ASBCB)
1071:(DBCLS)
1065:(COSBI)
979:Clustal
925:FlyBase
899:Ensembl
873:UniProt
855:GenBank
774:3322381
704:3334321
651:2672628
557:2705234
493:6200428
449:2690996
280:at the
269:History
249:Windows
201:Website
183:Windows
136:/bowtie
100: (
82: (
55:et al.,
1258:(CIBB)
1246:(ISMB)
1240:(ECCB)
1217:(JSBi)
1123:(NBIC)
1112:(NCBI)
1100:(JCVI)
1089:(EMBL)
1077:(DDBJ)
1031:ExPASy
1014:TopHat
994:MUSCLE
984:EMBOSS
974:Bowtie
949:GISAID
909:, and
881:TrEMBL
781:
771:
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658:
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321:TopHat
278:et al.
237:freely
221:Bowtie
146:github
130:github
125:Bowtie
74:Bowtie
20:Bowtie
1269:(PSB)
1191:(ISB)
1140:(SIB)
1129:(PGC)
1059:(CBD)
1023:Other
989:HMMER
969:BLAST
489:S2CID
306:SOAP2
245:macOS
241:Linux
179:macOS
175:Linux
951:and
917:BOLD
907:KEGG
883:and
865:and
779:PMID
734:2015
709:PMID
656:PMID
603:PMID
562:PMID
517:2013
454:PMID
337:fork
247:and
227:and
212:.net
190:Type
148:.com
132:.com
769:PMC
761:doi
699:PMC
691:doi
646:PMC
638:doi
593:doi
552:PMC
544:doi
481:doi
444:PMC
434:doi
294:DNA
231:in
206:www
163:C++
1435::
1234:()
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501:^
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430:10
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410:^
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370:.
265:.
243:,
143::
127::
832:e
825:t
818:v
785:.
763::
757:9
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