Search Results for: snakemake

Migrating from snakemake 7 to snakemake 8

I finally bit the bullet and migrated from snakemake 7 to snakemake 8. The short answer its not too hard! First, install the executor plugin for snakemake using mamba: Next, edit your config file and change the following: If you have a cluster: section, change that to cluster-generic-submit-cmd: Add the line: You need to remove […]

snakemake tutorial

There are a lot of snakemake tutorials out there to get you started: Intro to workflows for efficient automated data analysis, using snakemake This is a great introductory tutorial by Titus Brown at UC Davis GGG 298, Jan 2020 – Week 4 – snakemake for running workflows! is also by Titus and is a terrific […]

Wildcards in Snakemake

Snakemake is a versatile pipeline manager for doing a lot of bioinformatics analysis, but handling wildcards in snakemake is not transparent, and here are some tips and tricks that we have gathered to help you process lots of files easily.

minimap2 hints

Here are some tips and tricks for minimap2 that I keep forgetting! –split-prefix If you have a large (>4 GB) multisequence index file, there are two options. The first is to increase the value of -I when you build the index (preferred) so that the whole index is kept in memory. Note: This must be […]

command line deconseq

AKA: how to remove contamination from your metagenome! We use sharks genomes, but it works with humans, corals, and other things too! A while ago we wrote deconseq to allow you to remove contamination from your sequence libraries. We used an HTS-mapper to map the reads in your sequences to your reference genome, and then […]