fls-bioinformatics-core / auto_process_ngs

Scripts and utilities for automatic processing & management of Illumina NGS sequencing data.
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'make_fastqs': add specific protocol for Parse Evercode single cell data #952

Closed pjbriggs closed 6 months ago

pjbriggs commented 6 months ago

Adds a new Fastq generation protocol parse_evercode for use with Parse Evercode data.

The main difference from the standard protocol is that adapter trimming is disabled automatically when the new protocol is used, which is recommended by Parse. (When adapter trimming is applied erroneously then it can result in R2 reads which are shorter than 86bp, which causes Parse's downstream split-pipe analysis pipeline to reject those reads.)