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| Bowtie2 v2.5.4 | 05/16/24 |
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Please cite: Langmead B, Salzberg S. Fast gapped-read alignment with Bowtie 2. Nature Methods. 2012, 9:357-359. |
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Links
Indexes
All indexes are .bt2 format and are compatible with both Bowtie 2 and with Bowtie as of v1.2.3
Index storage is thanks to AWS Public Datasets program. See the Index zone page for details on the best ways to obtain this data, including from the AWS cloud.
Publications
- Langmead B, Salzberg S. Fast gapped-read alignment with Bowtie 2. Nature Methods. 2012, 9:357-359.
- Langmead B, Wilks C, Antonescu V, Charles R. Scaling read aligners to hundreds of threads on general-purpose processors. Bioinformatics Vol 35, Iss 3, 2019, pp 421–432.
Contributors
- Ben Langmead
- Daehwan Kim
- Rone Charles
- Nae-Chyun Chen
- Chris Wilks
- Valentin Antonescu
Tools that use Bowtie (or Bowtie 2):
- mRNA sequencing:
- Myrna (paper)
- TopHat, TopHat 2 (paper)
- Cufflinks (paper)
- Trinity (paper)
- MapSplice (paper)
- SpliceSeq (paper)
- RNASEQR (paper)
- RSEM (paper)
- GENE-counter (paper)
- RobiNA (paper)
- ExpressionPlot (paper)
- RUM (paper)
- BowStrap (paper)
- ContextMap (paper)
- eXpress (paper)
- ReXpress (paper)
- TrueSight (paper)
- PASTA (paper)
- QRNAseq
- Bisulfite-seq:
- BSmooth (paper)
- Bismark (paper)
- MethylCoder (paper)
- BS-Seeker (paper)
- B-SOLANA (paper)
- Bicycle
- Bison
- Re-seqeuncing:
- Assembly and scaffolding:
- Workflow:
- Galaxy (paper)
- Chipster (paper)
- GAPSS
- Unipro UGENE (paper)
- Biopieces
- InSilico DB (paper)
- LONI Pipeline (paper)
- KBase
- bioKepler
- Structural variants:
- Gene fusion:
- TopHat Fusion (paper)
- deFuse (paper)
- Comrad (paper)
- ShortFuse (paper)
- FusionHunter (paper)
- SnowShoes-FD (paper)
- FusionFinder (paper)
- Chimerascan (paper)
- FusionQ (paper)
- Metagenomics:
- Small RNA:
- isomiRID (paper)
- Deqor v3 (paper)
- NEXT-RNAi (design of genome-wide RNAi libraries)
- miREvo (paper)
- miRanalyzer (paper)
- MapMi (paper)
- shortran (paper)
- miRDeep2 (paper)
- YM500 (paper)
- starBase (paper)
- Other:
- PADUA (alignment of DNA to protein databases; paper)
- SeqTrimMap (sequential trimming and mapping; paper)
- mPrime (primer design)
- EMIGRE (ribosomal genes reconstruction; paper)
- TAPDANCE (identifies CISs in transposon junction fragment insertion data; paper)
- Paparazzi (reconstruction of viral genomes from small RNA reads; paper)
- CaPSID (pathogen detection; paper)
- EuPathDB (eukaryotic pathogen detection; paper)
OS distributions with Bowtie packages
Commercial products using Bowtie:
Published protocols using Bowtie 1 and/or 2:
- Wang S, et al. Target analysis by integration of transcriptome and ChIP-seq data with BETA. Nature Protocols.
- Hisano M, et al. Genome-wide chromatin analysis in mature mouse and human spermatozoa. Nature Protocols.
- Becker AH, et al. Selective ribosome profiling as a tool for studying the interaction of chaperones and targeting factors with nascent polypeptide chains and ribosomes. Nature Protocols.
- Anders S, et al. Count-based differential expression analysis of RNA sequencing data using R and Bioconductor. Nature Protocols.
- Wan Y, et al. Genome-wide mapping of RNA structure using nuclease digestion and high-throughput sequencing. Nature Protocols.
- Haas BJ, et al. De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nature Protocols.
- Ingolia NT, et al. Genome-Wide Annotation and Quantitation of Translation by Ribosome Profiling. Current Protocols in Molecular Biology.
- Baslan T, et al. Genome-wide copy number analysis of single cells. Nature Protocols.
- Trapnell C, et al. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nature Protocols.
- Ingolia NT, et al. The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments. Nature Protocols.
- Bardet AF, et al. A computational pipeline for comparative ChIP-seq analyses. Nature Protocols.
- Simon JS, et al. Using formaldehyde-assisted isolation of regulatory elements (FAIRE) to isolate active regulatory DNA. Nature Protocols.
- Goodman AL, et al. Identifying microbial fitness determinants by insertion sequencing using genome-wide transposon mutant libraries. Nature Protocols.
- Fanelli M, et al. Chromatin immunoprecipitation and high-throughput sequencing from paraffin-embedded pathology tissue. Nature Protocols.
- Christodoulou DC, et al.Quantification of Gene Transcripts with Deep Sequencing Analysis of Gene Expression (DSAGE) Using 1 to 2 micrograms Total RNA. Current Protocols in Molecular Biology.
