ddRADseq_reads preprocessing pipelines for STACKS

[Rafał Wóycicki]

Hi All,

I have prepared the ddRADseq_reads preprocessing pipelines to help running STACKS pipeline.

The pipelines in rafalwoycicki/ddRADseq_reads assist in preprocessing ddRADseq data — including adapter trimming, quality filtering, and deduplication — to prepare clean input files for STACKS analysis.

The new solution gave finally up to 10x more Stacks with Coverage 2-6 times higher than when preprocessing reads with the original proposed approach with STACKS's process_radtags and clone_filter. Comparison results in ComparisonFinal.ods (https://github.com/rafalwoycicki/ddRADseq_reads/blob/main/ComparisonsFinal.ods) file and in the Comparisons.md (https://github.com/rafalwoycicki/ddRADseq_reads/blob/main/Comparisons.md) file.

Hope it will be useful for all the users.

Best wishes,

Rafał