RFE: Quality trimming in the pipeline

nf-core / fastquorum

Pipeline to produce consensus reads using unique molecular indexes/barcodes (UMIs)

https://nf-co.re/fastquorum

MIT License

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RFE: Quality trimming in the pipeline #55

Open lbeltrame opened 4 months ago

lbeltrame commented 4 months ago

Description of feature

While not necessarily required, these can fit some recommended protocols by vendors like KAPA, (cf. "KAPA Bioinformatics Analysis for Longitudinal Detection of Circulating Tumor DNA"), where the non-UMI sequences are trimmed using fastp.

lbeltrame commented 4 months ago

Link to the protocol:

https://sequencing.roche.com/content/dam/diagnostics_microsites/sequencing/us/en/resources/pdfs/tech-note/MC-US-13753-External-KAPA-Bioinformatics-Analysis-for-Longitudinal-Detection-of-ctDNA.pdf