Sourmash

Compute MinHash signatures for DNA sequences.

Quick Start

To execute the pipeline on your computer, first pull the docker image

docker pull hadrieng/sourmash

Then execute the workflow

nextflow run sourmash.nf --reads data/\*.fastq

It will produce a directory containing a clustering & dendrogram of all the fastq files present in your data directory, as well as a similarity matrix and heatmap.

Pipeline parameters

--reads

• This parameter is required.
• Specifies the location of the reads fastq file

--adapt

• Optional.
• Specifies the location of the adapters file for adapter trimming
• It must end in .fasta
• By default it is set to data/adapters.fasta

Profiles

The SGBC cluster uses a module system. Pulling the docker image is not required!

By default, the pipeline runs locally using docker. If you run the nonpareil pipeline on the SGBC cluster, please pass the option -profile planet

Example:

nextflow run sourmash.nf -profile planet --reads /proj/my_proj/data/\*.fastq --adapt custom_adapters.fasta

Citations

• Buffalo Vince (2011), Scythe: A Bayesian adapter trimmer [Software]. Available at https://github.com/vsbuffalo/scythe
• Joshi NA, Fass JN. (2011). Sickle: A sliding-window, adaptive, quality-based trimming tool for FastQ files [Software].Available at https://github.com/najoshi/sickle.
• C. Titus Brown (2016). sourmash: a library for MinHash sketching of DNA. JOSS. doi: 10.21105/joss.00027