|Bowtie: Ultrafast short read alignment|
|Crossbow: Genotyping, cloud computing|
|Myrna: Cloud, differential gene expression|
|Tophat: RNA-Seq splice junction mapper|
|Cufflinks: Isoform assembly, quantitation|
|H. sapiens, UCSC hg18||3.5 GB|
|or: part 1 (1.5 GB), part 2 (651 MB), part 3 (1.5 GB)|
|H. sapiens, UCSC hg19||3.5 GB|
|or: part 1 (1.5 GB), part 2 (650 MB), part 3 (1.5 GB)|
|M. musculus, UCSC mm10||3.2 GB|
|or: part 1 (1.3 GB), part 2 (600 MB), part 3 (1.3 GB)|
|M. musculus, UCSC mm9||3.2 GB|
|or: part 1 (1.3 GB), part 2 (593 MB), part 3 (1.3 GB)|
|R. norvegicus, UCSC rn4||3.1 GB|
|or: part 1 (1.3 GB), part 2 (580 MB), part 3 (1.3 GB)|
Some unzip programs cannot handle archives >2 GB. If you have problems downloading or unzipping a >2 GB index, try downloading in parts.
- Langmead B, Salzberg S. Fast gapped-read alignment with Bowtie 2. Nature Methods. 2012, 9:357-359.
- 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.
Tools that use Bowtie 1 and/or 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)
- BSmooth (paper in press)
- Bismark (paper)
- MethylCoder (paper)
- BS-Seeker (paper)
- B-SOLANA (paper)
- Structural variants:
- Gene fusion:
- TopHat Fusion (paper)
- deFuse (paper)
- Comrad (paper)
- ShortFuse (paper)
- FusionHunter (paper)
- SnowShoes-FD (paper)
- FusionFinder (paper)
- Chimerascan (paper)
- SeqTrimMap (sequential trimming and mapping; paper)
- Deqor v3 (design and quality control of siRNAs; paper)
- NEXT-RNAi (design of genome-wide RNAi libraries)
- mPrime (primer design)
- EMIGRE (ribosomal genes reconstruction)
- MapMi (mapping and analysis of miRNAs; paper)
- TAPDANCE (identifies CISs in transposon junction fragment insertion data; paper)
- shortran (pipeline for small RNA-seq data analysis; paper)
- Paparazzi (reconstruction of viral genomes from small RNA reads; paper)
OS distributions with Bowtie packages
Commercial products using Bowtie:
Published protocols using Bowtie 1 and/or 2:
- 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.
- Goodman AL, et al. Identifying microbial fitness determinants by insertion sequencing using genome-wide transposon mutant libraries. 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.
- Fanelli M, et al. Chromatin immunoprecipitation and high-throughput sequencing from paraffin-embedded pathology tissue. Nature Protocols.
- Simon JS, et al. Using formaldehyde-assisted isolation of regulatory elements (FAIRE) to isolate active regulatory DNA. 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.