From the repository:

Minimizer based sparse de Bruijn Graph constructor. Homopolymer compress input sequences, pick syncmers from hpc-compressed sequences, connect syncmers with an edge if they are adjacent in a read, unitigify and homopolymer decompress. Suggested input is PacBio HiFi/CCS reads, or ONT duplex reads. May or may not work with Illumina reads. Not suggested for PacBio CLR or regular ONT reads

References:

• M. Rautiainen, T. Marschall. MBG: Minimizer-based Sparse de Bruijn Graph Construction. Genome Biology (2020). PubMed |  PMC |  Journal

• mbg on GitHub

• Module Name: mbg (see the modules page for more information)
• MBG is a multithreaded tool. Please match the number of allocated CPUs to the number of threads
• Example files in $MBG_TEST_DATA

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive --gres=lscratch:10 --cpus-per-task=2 --mem=3g
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]$ cd /lscratch/$SLURM_JOB_ID
[user@cn3144]$ module load mbg
[user@cn3144]$ cp ${MBG_TEST_DATA:-none}/SRR10971019.fasta .
[user@cn3144]$ MBG -t $SLURM_CPUS_PER_TASK -i SRR10971019.fasta -o SRR10971019_graph.gfa -k 1501 -w 1450 -a 1 -u 3
Parameters: k=1501,w=1450,a=1,u=3,t=2,r=0,R=0,hpcvariantcov=0,errormasking=hpc,endkmers=no,blunt=no,keepgaps=no,guesswork=no,cache=no
Collecting selected k-mers
Reading sequences from SRR10971019.fasta
1210730 total selected k-mers in reads
265228 distinct selected k-mers in reads
Unitigifying
Filtering by unitig coverage
3513 distinct selected k-mers in unitigs after filtering
Getting read paths
Reading sequences from SRR10971019.fasta
Building unitig sequences
Reading sequences from SRR10971019.fasta
Writing graph to SRR10971019_graph.gfa
selecting k-mers and building graph topology took 19,594 s
unitigifying took 0,81 s
filtering unitigs took 0,4 s
getting read paths took 19,186 s
building unitig sequences took 36,835 s
forcing edge consistency took 0,24 s
writing the graph and calculating stats took 0,94 s
nodes: 567
edges: 730
assembly size 5346906 bp, N50 29122
approximate number of k-mers ~ 4495839

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

Create a batch input file (e.g. mbg.sh), which uses the input file 'mbg.in'. For example:

#!/bin/bash
module load mbg/1.0.16
cp ${MBG_TEST_DATA:-none}/SRR10971019.fasta .
MBG -t $SLURM_CPUS_PER_TASK -i SRR10971019.fasta -o SRR10971019_graph.gfa -k 1501 -w 1450 -a 1 -u 3

Submit this job using the Slurm sbatch command.

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