RagTag is a collection of software tools for scaffolding and improving modern genome assemblies.

Tasks include:

• Homology-based misassembly correction
• Homology-based assembly scaffolding and patching
• Scaffold merging

Ragtag also provides command line utilities for working with common genome assembly file formats.

References:

• Alonge, Michael, et al. RaGOO: fast and accurate reference-guided scaffolding of draft genomes. Genome biology 20.1 (2019): 1-17.

• RagTag Main Site

• Module Name: ragtag (see the modules page for more information)
• singlethreaded
• Reference data in /data/genome/fasta/

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 ragtag

[user@cn3144 ~]$ ragtag.py --help

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

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

#!/bin/bash
set -e
module load ragtag
ragtag.py correct ref.fasta query.fasta

Submit this job using the Slurm sbatch command.

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

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

ragtag.py correct ref.fasta query1.fasta
ragtag.py correct ref.fasta query2.fasta
ragtag.py correct ref.fasta query3.fasta
ragtag.py correct ref.fasta query4.fasta

Submit this job using the swarm command.

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