CLAWS (CNAG's Long-read Assembly Workflow in Snakemake)

Snakemake Pipeline used for de novo genome assembly @CNAG. It has been developed for Snakemake v6.0.5.

It accepts Oxford Nanopore Technologies (ONT) reads, PacBio HFi reads, illumina paired-end data, illumina 10X data and Hi-C reads. It does the preprocessing of the reads, assembly, polishing, purge_dups, scaffolding, different evaluation steps and generation of pretext files for curation. Default behavior is to preprocess the reads, ...