kWIP-nf

A nextflow pipeline to estimate sample (dis)similarity using kWIP

Usage

To run on CBE:

module load nextflow/19.01.0
module load singularity/3.4.1

Single end:

nextflow run Gregor-Mendel-Institute/kWIP-nf --reads '/path/to/*fastq.gz' -profile cbe

Paired end:

nextflow run Gregor-Mendel-Institute/kWIP-nf --reads --pairedEnd '/path/to/*{1,2}*fastq.gz' -profile cbe

Parameters

• --reads (path to read(pair)s required)
• --pairedEnd (set if dealing with paired end reads default false)
• --trim (trim reads default true)
• --clip_r1 (bases to trim off 5' read 1 default 0)
• --clip_r2 (bases to trim off 5' read 2 default 0)
• --three_prime_clip_r1 (bases to trim off 3' read 1 default 0)
• --three_prime_clip_r1 (bases to trim off 3' read 2 default 0)
• --k_size (size of k-mers default 20)
• --tablesize (size of hashtable default 1e9)

Further reading

https://doi.org/10.1371/journal.pcbi.1005727

https://github.com/FelixKrueger/TrimGalore/blob/master/Docs/Trim_Galore_User_Guide.md

https://khmer.readthedocs.io

https://kwip.readthedocs.io