Seed-and-extend program for aligning long error-prone reads to genome graphs.

References:

• M. Rautiainen, T. Marschall. GraphAligner: rapid and versatile sequence-to-graph alignment. Genome Biology (2020). PubMed |  PMC |  Journal

• graphaligner on GitHub

• Module Name: graphaligner (see the modules page for more information)
• GraphAligner is a multithreaded application. Please match the number of threads with the number of allocated CPUs
• Example files in $GRAPHALIGNER_TEST_DATA

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

[user@biowulf]$ sinteractive --cpus-per-task=2 --gres=lscratch:10
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 graphaligner
[user@cn3144]$ cp -r ${GRAPHALIGNER_TEST_DATA:-none} test
[user@cn3144]$ GraphAligner -t $SLURM_CPUS_PER_TASK -g test/graph.gfa -f test/read.fa -a test/aln.gaf -x vg
[user@cn3144]$ cat test/aln.gaf
read    71      0       71      +       >1>2>4  87      3       73      67      72      60      NM:i:5  AS:f:56.3       dv:f:0.0694444  id:f:0.930556   cg:Z:4=1X2=1I38=1D5=1I5=1X13=

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

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

#!/bin/bash
module load graphaligner/1.0.18
GraphAligner -g $GRAPHALIGNER_TEST_DATA/graph.gfa -t $SLURM_CPUS_PER_TASK \
    -f $GRAPHALIGNER_TEST_DATA/read.fa -a aln.gaf -x vg

Submit this job using the Slurm sbatch command.

sbatch --cpus-per-task=2 graphaligner.sh

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

GraphAligner -g input1/graph.gfa -t $SLURM_CPUS_PER_TASK -f input1/read.fa -a output1/aln.gaf -x vg
GraphAligner -g input2/graph.gfa -t $SLURM_CPUS_PER_TASK -f input2/read.fa -a output2/aln.gaf -x vg

Submit this job using the swarm command.

swarm -f graphaligner.swarm -g 4 -t 2 --module graphaligner/1.0.16