Monopogen is an analysis package for SNV calling from single-cell sequencing, developed and maintained by Ken chen's lab in MDACC. Monopogen works on sequencing datasets generated from single cell RNA 10x 5', 10x 3', single ATAC-seq technoloiges, scDNA-seq etc.

References:

• Dou J. Single-nucleotide variant calling in single-cell sequencing data with Monopogen Nature Biotechnology. 2023 Aug 17:1-0.

• monopogen Github Site

This application requires a graphical connection using NX

• Module Name: monopogen (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
  • monopogen_HOME
• Example files in ???
• Reference data in /fdb/monopogen/

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 monopogen

[user@cn3144 ~]$  

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

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

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

Submit this job using the Slurm sbatch command.

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

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

monopogen < monopogen.in > monopogen.out
monopogen < monopogen.in > monopogen.out
monopogen < monopogen.in > monopogen.out
monopogen < monopogen.in > monopogen.out

Submit this job using the swarm command.

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