Bowtie

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Bowtie 1.3.1	09/13/21
Please cite: Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10:R25.
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Bowtie 2: Fast, accurate read alignment

Crossbow: Genotyping, cloud computing

Tophat: RNA-Seq splice junction mapper

Cufflinks: Isoform assembly, quantitation

Myrna: Cloud, differential gene expression

Lighter: Fast error correction

Other tools using Bowtie

Consider using Illumina's iGenomes collection. Each iGenomes archive contains pre-built Bowtie and Bowtie 2 indexes.

All indexes are for assemblies, not contigs. Unplaced or unlocalized sequences and alternate haplotype assemblies are excluded.

Some unzip programs cannot handle archives >2 GB. If you have problems downloading or unzipping a >2 GB index, try downloading in two parts.

Check .zip file integrity with MD5s.

• Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology 10:R25.
  
  
• Langmead B, Schatz M, Lin J, Pop M, Salzberg SL. Searching for SNPs with cloud computing. Genome Biology 10:R134.
  
  
• Trapnell C, Pachter L, Salzberg SL, TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 2009 25(9):1105-1111.

• Ben Langmead
• Cole Trapnell
• Daehwan Kim
• Rone Charles
• Chris Wilks
• Valentin Antonescu

• Papers citing Bowtie
• Johns Hopkins University
• JHU Computer Science