Hi All, I have written a simple BS-Seq aligner that wraps bwa mem. It is available from here: https://github.com/brentp/bwa-meth
There is a writeup of it here: http://arxiv.org/abs/1401.1129
In the paper, I did a comparison with bismark, Last, bsmap and gsnap. The calls that I used are here: https://github.com/brentp/bwa-meth/tree/master/compare in their respective run-*.sh files.
I will add gnumap-bs and further test bismark with bowtie 2 in the coming weeks.
As the intent is to find the best-case for each aligner, I welcome comments on the parameters I've chosen for the other aligners--in all cases I report the set of parameters that performed best of the ones I tested. Though, I'm sure there is room for improvement. I'd also appreciate feedback on what bismark parameters work well for bowtie2.
Finally, of course, I encourage use of and feedback on bwa-meth on paired-end BS-Seq reads, it works on both python2.7+ and python3.
There is a writeup of it here: http://arxiv.org/abs/1401.1129
In the paper, I did a comparison with bismark, Last, bsmap and gsnap. The calls that I used are here: https://github.com/brentp/bwa-meth/tree/master/compare in their respective run-*.sh files.
I will add gnumap-bs and further test bismark with bowtie 2 in the coming weeks.
As the intent is to find the best-case for each aligner, I welcome comments on the parameters I've chosen for the other aligners--in all cases I report the set of parameters that performed best of the ones I tested. Though, I'm sure there is room for improvement. I'd also appreciate feedback on what bismark parameters work well for bowtie2.
Finally, of course, I encourage use of and feedback on bwa-meth on paired-end BS-Seq reads, it works on both python2.7+ and python3.
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