hurwitzlab/centrifuge-patric

Name: centrifuge-patric

Owner: Hurwitz Lab

Description: Run Centrifuge on Stampede2 and get genomes for downstream applications

Created: 2018-04-24 18:50:10.0

Updated: 2018-04-26 23:31:30.0

Pushed: 2018-04-26 23:31:29.0

Homepage: null

Size: 34

Language: Python

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README

centrifuge-patric - Radcot Part One - YOU ARE HERE

• Identify bacterial species from a metagenomic sample
• Download genomes of said species

bowtie-samtools - Radcot Part Two - 2nd step

• Quantify transcripts of genes within these species

cuffdiff-keggR - Radcot Part Three - 3rd step

• Annotate RNA counts of genes with KEGG pathway information
• Generate graphs of RNA count differences per KEGG module

How to use:

1. Use https://www.imicrobe.us/#/apps to access the app with your cyverse login OR
2. git clone https://github.com/scottdaniel/centrifuge-patric
3. Get the singularity image like so: wget [address we setup]
4. Run the pipeline on an HPC with a slurm scheduler¹

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¹I assume this can be adapted to run on other batch-scheduled high-performance computer systems but this has not been tested.