The PhaseFinder algorithm is designed to detect DNA inversion mediated phase variation in bacterial genomes using genomic or metagenomic sequencing data. It works by identifying regions flanked by inverted repeats, mimicking their inversion in silico, and identifying regions where sequencing reads support both orientations. Here, we define phase variation as "a process employed by bacteria to generate frequent and reversible changes within specific hypermutable loci, introducing phenotypic diversity into clonal populations”. Not every region detected by PhaseFinder will directly result in phase variation, but the results should be highly enriched for regions that do.

References:

• Jiang X, Hall AB, et al. Invertible promoters mediate bacterial phase variation, antibiotic resistance, and host adaptation in the gut. Science (2019) DOI: 10.1126/science.aau5238

• PhaseFinder on GitHub

• Module Name: phasefinder (see the modules page for more information)
• PhaseFinder.py ratio multi-threaded with the -p/--threads flag.
• Environment variables set
  • PHASEFINDER_HOME
• Example files in $PHASEFINDER_HOME/data

Allocate an interactive session and run the program.
Sample session (user input in bold):

[user@biowulf]$ sinteractive -c 16
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load phasefinder

[user@cn3144 ~]$ PhaseFinder.py locate -f $PHASEFINDER_HOME/data/test.fa -t test.einverted.tab -g 15 85 -p

[user@cn3144 ~]$ PhaseFinder.py create -f $PHASEFINDER_HOME/data/test.fa -t test.einverted.tab -s 1000 -i test.ID.fasta

[user@cn3144 ~]$ PhaseFinder.py ratio -i test.ID.fasta -1 $PHASEFINDER_HOME/data/p1.fq -2 $PHASEFINDER_HOME/data/p2.fq -p $SLURM_CPUS_PER_TASK -o out

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Create a batch input file (e.g. phasefinder.sh). For example:

#!/bin/bash
set -e
module load phasefinder

PhaseFinder.py locate -f $PHASEFINDER_HOME/data/test.fa -t test.einverted.tab -g 15 85 -p

PhaseFinder.py create -f $PHASEFINDER_HOME/data/test.fa -t test.einverted.tab -s 1000 -i test.ID.fasta

PhaseFinder.py ratio -i test.ID.fasta -1 $PHASEFINDER_HOME/data/p1.fq -2 $PHASEFINDER_HOME/data/p2.fq -p $SLURM_CPUS_PER_TASK -o out

Submit this job using the Slurm sbatch command.

sbatch [--cpus-per-task=#] [--mem=#] phasefinder.sh

Create a swarmfile (e.g. phasefinder.swarm). For example:

PhaseFinder.py ratio -i test.ID.fasta -1 sample1_1.fq -2 sample1_2.fq -p $SLURM_CPUS_PER_TASK -o out
PhaseFinder.py ratio -i test.ID.fasta -1 sample2_1.fq -2 sample2_2.fq -p $SLURM_CPUS_PER_TASK -o out
PhaseFinder.py ratio -i test.ID.fasta -1 sample3_1.fq -2 sample3_2.fq -p $SLURM_CPUS_PER_TASK -o out
PhaseFinder.py ratio -i test.ID.fasta -1 sample4_1.fq -2 sample4_2.fq -p $SLURM_CPUS_PER_TASK -o out

Submit this job using the swarm command.

swarm -f phasefinder.swarm [-g #] [-t #] --module phasefinder