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tgen / phoenix

Jetstream compatible workflow template supporting comprehensive analysis of human sequencing data against GRCh38
MIT License
17 stars 6 forks source link

Feature: pcr free alignment #430

Closed bryce-turner closed 3 years ago

bryce-turner commented 3 years ago

This adds two new workflows designed with pcr free alignment in mind. The primary workflow uses bwa-mem2 and marks duplicates at the lane level before merging into one alignment file. We also have the fq2bam workflow which is gpu-accelerated, but this isn't called in the main.jst as it will likely be bottlenecked on our compute cluster.

bryce-turner commented 3 years ago

This resolves issue #384

bryce-turner commented 3 years ago

Good point, this is not configured for fasterq support, I'll add that now.