Bowtie1

Installation

• Download pre-compiled program from the website below.
  • Version 1.1.1 is available at http://sourceforge.net/projects/bowtie-bio/files/bowtie/1.1.1/
• Unzip the file. That's all you need.

Build a database

$ /path/to/bowtie/bowtie-build -f my_fasta_file db_name

Run it!

• Paired-end FASTQ reads

$ bowtie [options]* database_name -q --sam -1 sample_R1.fastq -2 sample_R2.fastq \
 > sample.db_name.sam

• Paired-end FASTQ reads, in crossbow-style (first 8 rows for R1, next 8 rows for R2, etc)

$ bowtie [options]* database_name -q --sam --12 sample_paired.fastq > sample.db_name.sam

• Single-end FASTQ reads

$ bowtie [options]* database_name -q --sam sample.fastq > sample.db_name.sam

• Single-end FASTA reads

$ bowtie [options]* database_name -f --sam sample.fastq > sample.db_name.sam

[options]

* Reporting:
  -k <int>           report up to <int> good alignments per read (default: 1)
  -a/--all           report all alignments per read (much slower than low -k)
  -m <int>           suppress all alignments if > <int> exist (def: no limit)
  -M <int>           like -m, but reports 1 random hit (MAPQ=0); requires --best
  --best             hits guaranteed best stratum; ties broken by quality
  --strata           hits in sub-optimal strata aren't reported (requires --best
* Performance:
  -o/--offrate <int> override offrate of index; must be >= index's offrate
  -p/--threads <int> number of alignment threads to launch (default: 1)
  --mm               use memory-mapped I/O for index; many 'bowtie's can share
  --shmem            use shared mem for index; many 'bowtie's can share

References

• Website - http://bowtie-bio.sourceforge.net/index.shtml
• Paper described detailed algorithms behind bowtie1 - http://genomebiology.com/2009/10/3/R25

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