Replace bwa with bwa-mem2 #50
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bwa-mem2 is the successor of the mem algorithm in bwa. It produces exactly the same results but is able to utilize more threads and recent x86 instruction sets like SSE4.1, AVX2 and AVX512. This required an additional indexing step but makes the alignment process up to three times faster.
For more details available here.
The indexing process is executed by running the following command from the root of the MIRACUM-Pipe installation dir:
cd assets/references/genome/ && ./../../tools/bwa-mem2/bwa-mem2 index genome.faAn already indexed genome could also be shipped with the
genome.fafile.