Introduction

Bowtie2 is a tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100 or 1000 of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes.

It is usually the first step in aligning the genomic (including identifying variation calling, ChIP-seq, RNA-seq, BS-seq) pipelines.

It can handle very long readings (for example, 10s or 100s of kilobytes), but it optimizes the length and error pattern of readings generated by recent sequencers, such as Illumina HiSeq 2000, Roche 454, and Ion Torrent instruments.

Bowtie2 indexes the genome with an FM Index (based on Burrows-Wheeler Transform or BWT) to keep its memory footprint small. For the human genome, the memory footprint is about 3.2 GB. Bowtie2 supports gapped, local, and end-to-end alignment modes. Multiple processors can be used at the same time to greatly improve the alignment speed.

For more information, visit the official Bowtie2 website.

Programming language: C

Brief description: A tool for aligning sequencing reads to long reference sequences

Open source license: GPL 3.0