Bowtie1 as the aligner of Bismark

FelixKrueger / SNPsplit

Allele-specific alignment sorting

http://felixkrueger.github.io/SNPsplit/

GNU General Public License v3.0

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Bowtie1 as the aligner of Bismark #76

Closed lelesama closed 1 year ago

lelesama commented 1 year ago

Hello

SNPsplit_User_Guide suggested the resulting .fa files are ready to be indexed with aligners including Bowtie2, Tophat, STAR, HISAT2, HiCUP and Bismark.

Could I use Bowtie1 as the aligner of Bismark?

FelixKrueger commented 1 year ago

No, I am afraid Bowtie 1 is:

a) not capable of aligning to N-masked genomes, and
b) no longer supported by Bismark as of 2019 or so