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@dnieuw showed fastp, a new preprocessing tool, see paper and code.
It might be able, in a single process, to eliminate the usage of trimmomatic, picard and fastqc. It handles all these functions into one process. Furthermore, it is compatible with MultiQC and it automatically accepts gzipped input files (and even outputs as gzipped files).
Should try it out, would speed up and simplify the pipeline greatly. Furthermore, it gives greater control over pre-processing and should play more nicely with Snakemake's DAG.
The text was updated successfully, but these errors were encountered:
@dnieuw showed
fastp
, a new preprocessing tool, see paper and code.It might be able, in a single process, to eliminate the usage of trimmomatic, picard and fastqc. It handles all these functions into one process. Furthermore, it is compatible with MultiQC and it automatically accepts gzipped input files (and even outputs as gzipped files).
Should try it out, would speed up and simplify the pipeline greatly. Furthermore, it gives greater control over pre-processing and should play more nicely with Snakemake's DAG.
The text was updated successfully, but these errors were encountered: