hurwitzlab/taxoner-patric

Name: taxoner-patric

Owner: Hurwitz Lab

Description: Uses taxoner64 and PATRIC bacterial database to map fastq/fasta to genomes

Created: 2015-10-27 21:39:30.0

Updated: 2016-01-12 22:46:24.0

Pushed: 2017-09-11 16:48:16.0

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Size: 1730

Language: Shell

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README

taxoner-patric

This is to work with taxoner64, a bowtie2 based solution to mapping reads to a metagenome

Google: https://code.google.com/p/taxoner/

Github: https://github.com/r78v10a07/taxoner

and with PATRIC, a database of bacterial genomes https://www.patricbrc.org/portal/portal/patric/Genomes

Patric genomes must be in bowtie2 format This is meant to be used on a PBS job scheduling system

Directions

1. Run the scripts in order, one at a time, in the /scripts dir
2. Check output and log files between each run
3. Any files named OPT- are considered optional steps
4. Enjoy!