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lentendu / DeltaMP

A flexible, reproducible and resource efficient metabarcoding amplicon pipeline for HPC
GNU General Public License v3.0
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Allow for possibility to truncate only based on expected error #163

Closed lentendu closed 1 year ago

lentendu commented 1 year ago

Which means filtering quality before pair-end merge, might be useful for gene with length heterogeneity, or libraries with low quality at 3'-end For TRUNCLEN == "no" and QFILT == "maxee", filtration is only done after pair-end merge. For TRUNCLEN == "xx" and QFILT == "maxee", filtration is done before pair-end merge, and optimization Introduce TRUNCBE: Truncation before pair-end

lentendu commented 1 year ago

Move filtering of MAXAMBIG and MAXHOMOP from fastq step to pair-end, opt and trim