Tandem repeat variations (TR-CNVs) are copy number variations of repeat units of tandem repeats (TRs). TRsv detects TR-CNVs within TR regions and structural variations (SVs) and short indels outside TR regions separately using long reads. The TR regions are defined using either a pre-built human TR bed file or user-prepared TR bed file. TRsv improves TR-CNV detection by assembling fragmented insertion and deletion alignments within a TR region of one long read alignment and searching for the TR units in the insertion sequence. In addition, TRsv improves SV detection derived from non-HiFi reads (PacBio CLR and Nanopore long reads) through machine learning-based filtering.

References:

• Kosugi, S., Terao, C. TRsv: simultaneous detection of tandem repeat variations, structural variations, and short indels using long read sequencing data. Genome Biol 26, 246 (2025).

• TRsv on GitHub

• Module Name: trsv (see the modules page for more information)
• Environment variables set
  • TRSV_HOME
• Template configuration files in $TRSV_HOME
• Example files in $TRSV_HOME/test_data

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

[user@biowulf]$ sinteractive --gres lscratch:1
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 trsv

[user@cn3144 ~]$ cd /lscratch/$SLURM_JOB_ID

[user@cn3144 ~]$ cp -r $TRSV_HOME/test_data/* .

[user@cn3144 ~]$ TRsv call -c config_hifi.txt

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

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

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

cp -r $TRSV_HOME/test_data/* .

TRsv call -c config_hifi.txt

Submit this job using the Slurm sbatch command.

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

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

TRsv call -c config1.txt
TRsv call -c config2.txt
TRsv call -c config3.txt

Submit this job using the swarm command.

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