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You could find the answers from official website: bowtie, and bowtie2

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.


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