#Instructions for using UGAP -Dependencies that MUST be installed by the user: 1. SPAdes, must be > version 3.5. Working on v3.7.1. 2. genomeCoverageBed (part of BEDTOOLS). Linux version included in /bin folder. If incompatible with your version, you must replace this version with your binary. 3. bwa (must have version that supports BWA-MEM algorithm). Tested version is 0.7.7 4. Samtools - tested version is 0.1.19 5. BioPython - tested version is -Optional dependencies for full functionality 1. BLAST+ (must have blastn in PATH). This is needed for troubleshooting mixtures 2. Musket (only if you want to correct reads with this tool); not thoroughly tested and may not work properly -To run: *You need a directory with paired-end reads in *.fastq.gz format. Names need to be similar to what comes off Illumina sequencer (e.g. *R1_001.fastq.gz) *You need to edit the "ugap_prep.py" script to reflect your installation location: Change this line to fit your directory: UGAP_PATH="/Users/jasonsahl/tools/UGAP" *First you will need to generate a UGAP input file. You can do this like: python ugap_prep.py -d reads -b /scratch/blastdb/nt -p 4 > ugap.config *If you don't give a path to a BLAST database, it will ignore this functionality. *Inspect the config file to make sure that you see commands that will be fed to UGAP *Submit to the queue using the "all" partition in this case. This will change depending on your own system python ugap_univeral_controller.py -c ugap.config -o slurm -q all
Created by: Darrin Lemmer
Modified on: Fri, Mar 3, 2017 at 11:42 AM
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