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dpryan79 / MethylDackel

A (mostly) universal methylation extractor for BS-seq experiments.
MIT License
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best bisulfite treated reads aligner to choose #40

Closed lmanchon closed 7 years ago

lmanchon commented 7 years ago

--Hi,

which bisulfite reads aligner do you recommend to then use MethylDackel, several aligners exist:

bwa-meth: https://github.com/brentp/bwa-meth ERNE-BS5: http://erne.sourceforge.net/ RMAPBS used in MethPipe (http://smithlabresearch.org/software/methpipe/) Bismark (http://www.bioinformatics.babraham.ac.uk/projects/bismark/) Bison (https://sourceforge.net/projects/dna-bison/)

thank you --

dpryan79 commented 7 years ago

bwa-meth is quite good and easy to install. I wrote bison, which is also quite good but very much not easy to install. I've never used ERNE-BS5 or RMAPBS. Bismark is OK, but quite slow.

At the end of the day, it shouldn't make a huge difference.

lmanchon commented 7 years ago

yes, i confirm bison isn't easy to install with mpi lib, is it possible to install without mpi lib ?

dpryan79 commented 7 years ago

No, it's specifically for clusters using MPI.

lmanchon commented 7 years ago

ok, thanks