How is Bowtie 2 different from Bowtie 1?
Bowtie 1 was released in 2009 and was geared toward aligning the
relatively short type of sequencing reads (up to 50 bp) prevalent at
the time. Since then, sequencing technology has improved both in terms
of throughput (more bp produced per sequencer per day) and in terms of
read length (more bp per read). Chief differences between Bowtie 1 and
Bowtie 2 are:
- Bowtie 2 fully supports gapped alignment with affine gap
penalties. Number of gaps and gap lengths are not restricted, except
via the user-supplied scoring scheme. Bowtie 1 only finds ungapped
- For reads longer than about 50 bp Bowtie 2 is generally
faster, more sensitive, and uses less memory than Bowtie 1. For
relatively short reads (e.g. less than 50 bp) Bowtie 1 is sometimes
faster and/or more sensitive.
- Bowtie 2 supports a "local" alignment mode, which doesn't require
that reads align end-to-end. This produces
alignments that might be "trimmed" (or "soft clipped") at one or both
extremes in a way that optimizes alignment score. Bowtie 2 also
supports an "end-to-end" alignment mode which, like Bowtie 1, requires
that the read align entirely.
- There is no upper limit on read length in Bowtie 2. Bowtie 1
had an upper limit of around 1000 bp.
- Bowtie 2 does away with Bowtie 1's notion of alignment "stratum". In Bowtie 2
all alignments lie along a continuous spectrum of alignment scores.
- There is no longer a distinction between "end-to-end" and "Maq-like"
modes as in Bowtie 1. There is just one scoring scheme, similar to
Needleman-Wunsch and Smith-Waterman.
- Bowtie 2's paired-end alignment
mode is more flexible than Bowtie 1's. For example, for pairs that do
not align in a paired fashion, it will attempt to find unpaired
alignments for each mate.
- Bowtie 2 does not align colorspace reads.