From the pangenome user manual:
nf-core/pangenome is a bioinformatics best-practise analysis pipeline for the rendering of a collection of sequences into a pangenome graph. Its goal is to build a graph that is locally directed and acyclic while preserving large-scale variation. Maintaining local linearity is important for interpretation, visualization, mapping, comparative genomics, and reuse of pangenome graphs.
[user@nc3144]$ module load pangenome
[user@nc3144]$ vg
$PANGENOME_TEST_DATAAllocate an interactive session and run the program. Sample session:
Allocate an interactive session with sinteractive and use as shown below. In this case we will use test data that is an artificial mixture of 1M human exome reads and 1M environmental metagenomic reads. The 50% human reads is treated as an artificial contamination and removed:
[user@biowulf]$ sinteractive --mem=36g --cpus-per-task=12 --gres=lscratch:10
salloc.exe: Pending job allocation 33247354
salloc.exe: job 33247354 queued and waiting for resources
salloc.exe: job 33247354 has been allocated resources
salloc.exe: Granted job allocation 33247354
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job
srun: error: x11: no local DISPLAY defined, skipping
[user@nc3144]$ module load pangenome
[user@nc3144]$ cd /lscratch/${SLURM_JOB_ID}
[user@nc3144]$ vg
vg: variation graph tool, version v1.40.0 "Suardi"
usage: /usr/local/bin/vg [options]
main mapping and calling pipeline:
-- autoindex mapping tool-oriented index construction from interchange formats
-- construct graph construction
-- rna construct splicing graphs and pantranscriptomes
-- index index graphs or alignments for random access or mapping
-- map MEM-based read alignment
-- giraffe fast haplotype-aware short read alignment
-- mpmap splice-aware multipath alignment of short reads
-- augment augment a graph from an alignment
-- pack convert alignments to a compact coverage index
-- call call or genotype VCF variants
-- help show all subcommands
For more commands, type `vg help`.
For technical support, please visit: https://www.biostars.org/t/vg/
[user@nc3144]$ pggb
[user@nc3144]$ odgi
odgi: optimized dynamic genome/graph implementation, version v0.8.3-0-g34f006f3
usage: /usr/local/bin/odgi [options]
Overview of available commands:
-- bin Binning of pangenome sequence and path information in the graph.
-- break Break cycles in the graph and drop its paths.
-- build Construct a dynamic succinct variation graph in ODGI format from a GFAv1.
-- chop Divide nodes into smaller pieces preserving node topology and order.
-- cover Cover the graph with paths.
-- crush Crush runs of N.
-- degree Describe the graph in terms of node degree.
-- depth Find the depth of a graph as defined by query criteria.
-- draw Draw previously-determined 2D layouts of the graph with diverse annotations.
-- explode Breaks a graph into connected components storing each component in its own file.
-- extract Extract subgraphs or parts of a graph defined by query criteria.
-- flatten Generate linearizations of a graph.
-- flip Flip path orientations to match the graph.
-- groom Harmonize node orientations.
-- heaps Path pangenome coverage permutations.
-- inject Inject BED annotations as paths.
-- kmers Display and characterize the kmer space of a graph.
-- layout Establish 2D layouts of the graph using path-guided stochastic gradient descent.
-- matrix Write the graph topology in sparse matrix format.
-- normalize Compact unitigs and simplify redundant furcations.
-- overlap Find the paths touched by given input paths.
-- panpos Get the pangenome position of a given path and nucleotide position (1-based).
-- pathindex Create a path index for a given graph.
-- paths Interrogate the embedded paths of a graph.
-- pav Presence/absence variants (PAVs).
-- position Find, translate, and liftover graph and path positions between graphs.
-- priv Differentially private sampling of graph subpaths.
-- procbed Procrustes-BED: adjust BED to match subpaths in graph.
-- prune Remove parts of the graph.
-- server Start a basic HTTP server to lift coordinates between path and pangenomic positions.
-- similarity Provides a sparse similarity matrix for paths or groups of paths.
-- sort Apply different kind of sorting algorithms to a graph.
-- squeeze Squeezes multiple graphs in ODGI format into the same file in ODGI format.
-- stats Metrics describing a variation graph and its path relationship.
-- stepindex Generate a step index and access the position of each step of each path once.
-- tension evaluate the tension of a graph helping to locate structural variants and abnormalities
-- tips Identifying break point positions relative to given references.
-- unchop Merge unitigs into a single node preserving the node order.
-- unitig Output unitigs of the graph.
-- untangle Project paths into reference-relative, to decompose paralogy relationships.
-- validate Validate a graph checking if the paths are consistent with the graph topology.
-- version Print the version of ODGI to stdout.
-- view Project a graph into other formats.
-- viz Visualize a variation graph in 1D.
[user@nc3144]$ # copy test data
[user@nc3144]$ cp $PANGENOME_TEST_DATA/* .
[user@nc3144]$ cp /usr/local/apps/nextflow/nextflow.config .
[user@nc3144]$ # run pangenome on the test data with biowulflocal profile
[user@nc3144]$ nextflow run nf-core/pangenome \
-r dev -profile biowulflocal \
--input DRB1-3123.fa.gz \
--n_haplotypes 12 \
--outdir testout \
-with-singularity $PANGENOME_PATH/pangenome.img
[user@nc3144]$ exit
[user@biowulf]$
Create a batch input file (e.g. pangenome.sh) similar to the following example:
#! /bin/bash
module load pangenome || exit 1
if [[ ! -e DRB1-3123.fa.gz ]]; then
cp $PANGENOME_TEST_DATA/* .
fi
cp /usr/local/apps/nextflow/nextflow.config .
nextflow run nf-core/pangenome \
-r 1.0.0 -profile biowulf \
--input DRB1-3123.fa.gz \
--n_haplotypes 12 \
--outdir testout \
-with-singularity $PANGENOME_PATH/pangenome.img
Submit this job using the Slurm sbatch command.
sbatch --cpus-per-task=12 --mem=72g --gres=lscratch:10 pangenome.sh