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UPHL-BioNGS / Cecret

Reference-based consensus creation
MIT License
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Adding MPX PrimalSeq bedfiles #125

Closed tives82 closed 1 year ago

tives82 commented 1 year ago

This PR includes the addition of a mpx_primalseq profile to Cecret, which includes the addition of the primalseq primer bedfile, primalseq amplicon bedfile, and updating the Monkeypox section of the Readme. Monkeypox virus multiplexed PCR amplicon sequencing (PrimalSeq)

tives82 commented 1 year ago

This looks great!

Do you have some SRA accessions of 3-5 MPX sequences with the primalseq primers? I want to test this before merging.

I've added some to /Volumes/IDGenomics_NAS/MPXV/primalseq_testing_reads for you to test. I also ran cecret on them with the primalseq primers so you'll notice the output and work directories there as well. cecret_results.csv

erinyoung commented 1 year ago

PrimalSeq_trimming

It looks like the primer file works! (This is the

NC_063383.1 2606    2628    MPXV_3_LEFT 1   +

primer region)