Straglr is a tool that can be used for genome-wide scans for tandem repeat(TR) expansions or targeted genotyping using long-read alignments.

References:

• Chiu R. Straglr: discovering and genotyping tandem repeat expansions using whole genome long-read sequences. Genome Biol 22, 224 (2021).

• straglr Main Site

This application requires a graphical connection using NX

• Module Name: straglr (see the modules page for more information)
• Multithreaded/singlethreaded/MPI...
• This application produces HTML reports. You can use hpcdrive to view these reports on your local workstation.
• Environment variables set
  • STRAGLR_TEST_DATA
• Example files in STRAGLR_TEST_DATA

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

[user@biowulf]$ sinteractive
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 straglr
[user@cn3144 ~]$ cp -r ${STRAGLR_TEST_DATA} . ; cd test_data 
[user@cn3144 ~]$ straglr.py test.bam /fdb/igenomes/Homo_sapiens/UCSC/hg38/Sequence/WholeGenomeFasta/genome.fa straglr_scan --min_str_len 2 --max_str_len 100 --min_ins_size 100 --genotype_in_size  --min_support 2 --max_num_clusters 2    

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

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

#!/bin/bash
set -e
module load straglr
straglr < straglr.in > straglr.out

Submit this job using the Slurm sbatch command.

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

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

straglr < straglr.in > straglr.out
straglr < straglr.in > straglr.out
straglr < straglr.in > straglr.out
straglr < straglr.in > straglr.out

Submit this job using the swarm command.

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