A readtrimming and quality control pipeline
Project description
multitrim
Author: Kenji Gerhardt Email: Kenji.Gerhardt@gmail.com Github: https://github.com/KGerhardt/multitrim User Manual: https://docs.google.com/document/d/13Oiu5UH6UTZ8lZWgO34ehj-wwZRVKwdVipqdh_qAiLE/edit?usp=sharing
Multitrim is a pipeline for Illumina short read trimming and quality control.
Multitrim accepts both single-end and paired-end reads and does the following:
- Subsamples up to 100k reads from each read file
- Detects adapter presence in the subsample(s) and records the sufficiently present adapter sequences by Illumina kit
- Trims input reads with FaQCs and detected adapters
- Retrims the FaQCs output with fastp and detected adapters
- Uses Falco to create FastQC-like quality reports for pre-trim and post-trim reads
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