## 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:

- Crossbow (paper)

- Assembly and scaffolding:

- Zorro
- SSPACE (paper)
- TIGER (paper)

- Workflow:

- Galaxy (paper)
- Chipster (paper)
- GAPSS
- Unipro UGENE (paper)
- Biopieces
- InSilico DB (paper)
- LONI Pipeline (paper)
- KBase
- bioKepler

- Structural variants:

- nFuse (paper)

- Gene fusion:

- TopHat Fusion (paper)
- deFuse (paper)
- Comrad (paper)
- ShortFuse (paper)
- FusionHunter (paper)
- SnowShoes-FD (paper)
- FusionFinder (paper)
- Chimerascan (paper)
- FusionQ (paper)

- Metagenomics:

- Genometa (paper)
- MetaPhlan (paper)
- MG-RAST (paper)
- metAMOS (paper)

- 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

- Ubuntu
- Debian
- Fedora
- MacPorts

## Commercial products using Bowtie:

- Geospiza GeneSifter
- CLC Genomics Server
- Partek Flow
- SevenBridges genomics
- Appistry
- Maverix Biomics

## 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.