Instructions for using UGAP

Dependencies for UGAP include:

1. SPAdes
2. bwa (must have version that supports BWA-MEM algorithm).
3. Samtools
4. BioPython
5. blast+ (optional)
6. bbmap
7. seqtk
8. bedtools

Installing with conda

conda create -n ugap python=3.7
conda activate ugap
conda install -c conda-forge mamba
mamba install -c bioconda spades bwa samtools biopython blast bbmap seqtk bedtools
mamba install -c anaconda pigz
git clone https://github.com/jasonsahl/UGAP.git

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). Single end support has not been thoroughly tested

*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 and run the “sendsketch” method in bbmap instead

*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