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We would like to announce that Bismark has received a major overhaul. While the default alignment behaviour of Bismark (using Bowtie 1) has not changed very much (see below), Bismark does now also support gapped alignments using Bowtie 2. From all test we have performed so far (single or paired-end, directional or non-directional with various simulated methylation levels or real life datasets) the Bismark results of both Bowtie 1 and Bowtie 2 are very concordant.
However, as Bowtie 2 is still in beta and subject to change, the current release of Bismark has therefore also to be considered a beta version (0.6.beta1).
Here is an overview of the most prominent changes:
Running Bismark with Bowtie 1 (default)
- Default output changed to SAM format
- The ‘old’ output format is still available via the option ‘--vanilla’
- Alignment processes were slightly modified to run in --norc/--nofw mode where appropriate, which may result in a slightly increased mapping efficiencies
- The former option ‘--directional’ is now the new default mode (‘--non_directional’ will report alignments to all four strands)
- The default paired-end maximum insert size ('-X') was increased to 500bp (up from 250bp)
Running Bismark with Bowtie 2 (optional)
- Alignments are performed in end-to-end mode (similar to Bowtie 1), but do allow gapped alignments with insertions and/or deletions
- Output format is SAM
- Since Bowtie 2 requires different indexes for alignments, the bismark genome preparation does now also support Bowtie 2 bisulfite indexing of a reference genome
I should like to stress that we don’t think that using Bowtie 2 for Bismark alignments is simply a replacement for Bowtie 1. Rather, as is also stated on the project its page, Bowtie 2 is supposed to work more efficiently for longer reads and allows gapped alignments. For shorter and/or indel-free reads Bowtie 1 may well be faster and more accurate, which is why Bowtie 1 will remain the default alignment mode for Bismark. Indeed, in some of the tests I have run so far the Bowtie 1 seemed to have a speed advantage.
While Bismark seems to work fine in all alignments modes, its methylation_extractor works currently only on the old Bowtie 1 (‘--vanilla’) output and not yet on SAM output files (I am going to work on this in the next couple of days/weeks). This is another reason for calling the current Bismark version 0.6.beta1.
Compared to Bowtie 1, Bowtie 2 has many ‘new’ parameters, of which the following are currently adjustable:
-M <int> (reporting the best out of N valid alignments)
-N <int> (multi-seed mismatches)
-L <int> (seed length)
-D <int> (maximum number of seed extension fail tries)
-R <int> (reseeding of repetitive alignments)
--score-min <func> (setting minimum alignment score for valid alignments)
We are still in the process of determining a set of most sensible parameters to generate unique 'best' alignments in a reasonable time (inceasing some of the parameters above might make Bismark run dog slow...). I would very much appreciate any comments or input in this regard (and of course also bug reports...).
All files are available from the Bismark project page.
Thanks,
Felix
However, as Bowtie 2 is still in beta and subject to change, the current release of Bismark has therefore also to be considered a beta version (0.6.beta1).
Here is an overview of the most prominent changes:
Running Bismark with Bowtie 1 (default)
- Default output changed to SAM format
- The ‘old’ output format is still available via the option ‘--vanilla’
- Alignment processes were slightly modified to run in --norc/--nofw mode where appropriate, which may result in a slightly increased mapping efficiencies
- The former option ‘--directional’ is now the new default mode (‘--non_directional’ will report alignments to all four strands)
- The default paired-end maximum insert size ('-X') was increased to 500bp (up from 250bp)
Running Bismark with Bowtie 2 (optional)
- Alignments are performed in end-to-end mode (similar to Bowtie 1), but do allow gapped alignments with insertions and/or deletions
- Output format is SAM
- Since Bowtie 2 requires different indexes for alignments, the bismark genome preparation does now also support Bowtie 2 bisulfite indexing of a reference genome
I should like to stress that we don’t think that using Bowtie 2 for Bismark alignments is simply a replacement for Bowtie 1. Rather, as is also stated on the project its page, Bowtie 2 is supposed to work more efficiently for longer reads and allows gapped alignments. For shorter and/or indel-free reads Bowtie 1 may well be faster and more accurate, which is why Bowtie 1 will remain the default alignment mode for Bismark. Indeed, in some of the tests I have run so far the Bowtie 1 seemed to have a speed advantage.
While Bismark seems to work fine in all alignments modes, its methylation_extractor works currently only on the old Bowtie 1 (‘--vanilla’) output and not yet on SAM output files (I am going to work on this in the next couple of days/weeks). This is another reason for calling the current Bismark version 0.6.beta1.
Compared to Bowtie 1, Bowtie 2 has many ‘new’ parameters, of which the following are currently adjustable:
-M <int> (reporting the best out of N valid alignments)
-N <int> (multi-seed mismatches)
-L <int> (seed length)
-D <int> (maximum number of seed extension fail tries)
-R <int> (reseeding of repetitive alignments)
--score-min <func> (setting minimum alignment score for valid alignments)
We are still in the process of determining a set of most sensible parameters to generate unique 'best' alignments in a reasonable time (inceasing some of the parameters above might make Bismark run dog slow...). I would very much appreciate any comments or input in this regard (and of course also bug reports...).
All files are available from the Bismark project page.
Thanks,
Felix
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