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fulcrumgenomics / fgbio

Tools for working with genomic and high throughput sequencing data.
http://fulcrumgenomics.github.io/fgbio/
MIT License
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2 Alignment steps #970

Closed shashwatsahay closed 6 months ago

shashwatsahay commented 6 months ago

Hi

Is it necessary to align the sequence twice? My files are quite large takes approx 8 hours for one run of bwa mem.

Can we skip the alignement step in Step 1.2 of https://github.com/fulcrumgenomics/fgbio/blob/main/docs/best-practice-consensus-pipeline.md and directly proceed to GroupReadsByUmi and start the downstreams Phase 2 steps.

Any insights into why the prealignment is necessary will be helpful

nh13 commented 6 months ago

Yes it is required, do you have someone that can help you at your organization to help mentor you why? We're available for consulting too: https://www.fulcrumgenomics.com/