The purpose of this repsoitory is to consolidate numerous CHTC/HT condor submit files created by members of the microbiome community on UW-Madison campus to analyze their own microbiome data using High throughput computing.

Follow this link to find a template on how to add submit files to this site.

Submit files

Run Many ANI comparisons on CHTC

This workflow runs many ANI comparisons, pairwise within sets of directories. It will run all pairwise comparisons for the fasta files that end in *.fna within each directory.
Contact Sarah Stevens

Pipeline for running checkm on UW-Madison’s CHTC or an HTCondor system

This pipeline includes scripts for running checkm on a group of genomes and getting back a group of files for each genome containing the completeness and redundancy results. This pipeline is written for an HTCondor system, specifically UW-Madison’s CHTC’s HPC cluster using this docker image for checkm.
Contact Sarah Stevens

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