ctmrbio/sourmash_sketch

Compare samples based on kmers using Sourmash sketch

CTMR's Nextflow sourmash sketcher

This Nextflow workflow allows you to easily compute Sourmash sketches to make kmer-based comparisons of samples.

Note that it only uses the forward read of each sample to compute the sketch.

The default output directory is results. It is possible to change output directory by specifying --outdir FOLDERNAME.

How to run locally

nextflow run ctmrbio/sourmash_sketch --reads 'path/to/reads/*_{1,2}.fq.gz' 

This will use whatever environment you currently have activated. To run with conda add -profile conda to the command line.

How to run on Gandalf

nextflow run ctmrbio/sourmash_sketch --reads 'path/to/reads/*_{1,2}.fq.gz' -profile gandalf 

Note that there is only a single - in -profile (this sends this argument to Nextflow instead of the workflow).

Output files

Three types of output are produced, one folder containing the individual sample sketches, one comparison matrix in binary NumPy format, and some plots.