Read alignment and variants · Software
Bowtie 2
Aligns sequencing reads to long reference genomes using memory-efficient FM indexing.
What Bowtie 2 is
Bowtie 2 is a tool for aligning sequencing reads to long reference sequences, such as mammalian genomes. It matches read sequences against a reference to infer where the reads originated, supporting reads ranging from approximately 50 characters to hundreds or thousands of base pairs.
The software addresses the computational challenge of searching large genomes by indexing references with an FM Index. This keeps the memory requirement low, typically consuming around 3.2 GB of RAM when aligning against the human genome.
Originally introduced by Ben Langmead and Steven Salzberg, Bowtie 2 produces alignments in SAM format and supports unpaired or paired-end reads across varied alignment criteria.
How it works
Bowtie 2 uses reference indexes generated by its companion utility, bowtie2-build. The indexer converts reference FASTA sequences into a set of six files ending in .bt2 (or .bt2l for large indexes), implementing an FM Index based on opportunistic data structures. Once created, the original FASTA files are no longer required for alignment.
During alignment, the bowtie2 program aligns read files to the index using gapped, local, or paired-end modes. The package also includes bowtie2-inspect, which reads an existing index to extract summary statistics, sequence names, or the underlying reference sequences.
Key facts
- Software version
- 2.5.4
- Index type
- FM Index (.bt2, .bt2l)
- Input formats
- FASTA (references), FASTQ / read files (unpaired or paired)
- Output format
- SAM
- Human genome memory footprint
- Approximately 3.2 GB
- Supported alignment modes
- Gapped, local, paired-end, and unpaired
What you can use it for
- Reference genome alignment
- Aligning single-end or paired-end sequencing reads of 50 to thousands of bases to mammalian or other long genomes.
- Gapped and local alignment
- Mapping reads that require insertion and deletion handling or local matching against the reference sequence.
- Index inspection and reconstruction
- Extracting reference sequences, reference names, or summary metrics directly from pre-built Bowtie 2 index files.
Run it here
Bowtie 2 is preinstalled on the machine behind every research conversation. Ask the agent in plain language, or give it the exact command — it runs it, reads the output and explains it.
Strengths and limits
Good at
- Low memory usage, needing around 3.2 GB of RAM for the human genome.
- Supports multiple alignment configurations, including gapped, local, and paired-end modes.
- Accommodates a wide range of read lengths, from 50 to thousands of characters.
Watch out for
- Index files are incompatible with Bowtie 1 .ebwt indexes.
- Ambiguous or repetitive reference regions can prevent finding a single definitive alignment location for a read.
Questions
Can I run Bowtie 2 online without installing it?
Bowtie 2 is preinstalled on the machine behind every research conversation. Ask the agent in plain language, or give it the exact command — it runs it, reads the output and explains it.
What licence is Bowtie 2 under?
Bowtie 2 is published under its authors' own licence; the project page at https://bowtie-bio.sourceforge.net/bowtie2/ states it.
What read lengths does Bowtie 2 support?
It is suited for reads starting around 50 characters up to hundreds or thousands of characters.
Can Bowtie 2 read Bowtie 1 index files?
No, Bowtie 2 utilizes its own .bt2 or .bt2l index format, which is not compatible with Bowtie 1 .ebwt indexes.
What output format does Bowtie 2 provide?
Bowtie 2 outputs alignment results in the standard SAM format.
What hardware memory is required for human genome alignment?
Aligning reads against the human genome typically requires approximately 3.2 GB of memory.
How to cite it
Langmead B, Salzberg S. Fast gapped-read alignment with Bowtie 2. Nature Methods. 2012, 9:357-359.
Written from Bowtie 2's own README and project page. Statements citing a figure that does not appear there are removed before publication. Licence and running details come from our registry.