bwa-mem2 support - Githubissues

DKFZ-ODCF / AlignmentAndQCWorkflows

The DKFZ alignment workflow plugin originally developed at the eilslabs

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Open vinjana opened 3 years ago

vinjana commented 3 years ago

bwa-mem2 is 1.7-2 times faster with ~2 times more memory. For time-critical data bwa-mem2 should be used.

bwa-mem2 command (CLI) seems to be compatible to bwa-mem. Therefore,

Change binary name and module load
Adapt conda environment
Is there anything necessary except for the path to the FASTA for working with bwa-mem2 reference genomes?