Description from the GitHub repo

Evaluate genome assemblies with k-mers and more
Often, genome assembly projects have illumina whole genome sequencing reads available for the assembled individual. The k-mer spectrum of this read set can be used for independently evaluating assembly quality without the need of a high quality reference. Merqury provides a set of tools for this purpose.

References:

• A. Rhie, B. P. Walenz, S. Koren et al. Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies. Genome Biol (2020). PubMed |  PMC |  Journal

• merqury on GitHub

• Module Name: merqury (see the modules page for more information)
• Best run with approximately 6 CPUs in local mode.
• Example files in $MERQURY_TEST_DATA

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

[user@biowulf]$ sinteractive --mem=10g --cpus-per-task=6 --gres=lscratch:20
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 merqury
[user@cn3144]$ cp ${MERQURY_TEST_DATA:-none}/* .
[user@cn3144]$ for f in *.tar.gz ; do tar -xzf $f ; done
[user@cn3144]$ merqury.sh F1.k18.meryl col0.hapmer.meryl cvi0.hapmer.meryl athal_COL.fasta athal_CVI.fasta test
[user@cn3144]$ ls test*
test.athal_COL.100_20000.phased_block.bed       test.athal_COL.spectra-cn.fl.png                test.athal_CVI.cvi0.hapmer.wig
test.athal_COL.100_20000.phased_block.blob.png  test.athal_COL.spectra-cn.hist                  test.athal_CVI.only.hist
test.athal_COL.100_20000.phased_block.counts    test.athal_COL.spectra-cn.ln.png                test.athal_CVI.qv
test.athal_COL.100_20000.phased_block.sizes     test.athal_COL.spectra-cn.st.png                test.athal_CVI.sort.bed
test.athal_COL.100_20000.phased_block.stats     test.athal_CVI.100_20000.phased_block.bed       test.athal_CVI.spectra-cn.fl.png
test.athal_COL.100_20000.switch.bed             test.athal_CVI.100_20000.phased_block.blob.png  test.athal_CVI.spectra-cn.hist
test.athal_COL.100_20000.switches.txt           test.athal_CVI.100_20000.phased_block.counts    test.athal_CVI.spectra-cn.ln.png
test.athal_COL.block.N.png                      test.athal_CVI.100_20000.phased_block.sizes     test.athal_CVI.spectra-cn.st.png
test.athal_COL.col0.hapmer.spectra-cn.fl.png    test.athal_CVI.100_20000.phased_block.stats     test.completeness.stats
test.athal_COL.col0.hapmer.spectra-cn.ln.png    test.athal_CVI.100_20000.switch.bed             test.dist_only.hist
test.athal_COL.col0.hapmer.spectra-cn.st.png    test.athal_CVI.100_20000.switches.txt           test.hapmers.blob.png
test.athal_COL.col0.hapmer.spectra-hap-cn.hist  test.athal_CVI.block.N.png                      test.hapmers.count
test.athal_COL.col0.hapmer.wig                  test.athal_CVI.col0.hapmer.spectra-cn.fl.png    test.only.hist
test.athal_COL.contig.sizes                     test.athal_CVI.col0.hapmer.spectra-cn.ln.png    test.qv
test.athal_COL.continuity.N.png                 test.athal_CVI.col0.hapmer.spectra-cn.st.png    test.spectra-asm.fl.png
test.athal_COL.cvi0.hapmer.spectra-cn.fl.png    test.athal_CVI.col0.hapmer.spectra-hap-cn.hist  test.spectra-asm.hist
test.athal_COL.cvi0.hapmer.spectra-cn.ln.png    test.athal_CVI.col0.hapmer.wig                  test.spectra-asm.ln.png
test.athal_COL.cvi0.hapmer.spectra-cn.st.png    test.athal_CVI.contig.sizes                     test.spectra-asm.st.png
test.athal_COL.cvi0.hapmer.spectra-hap-cn.hist  test.athal_CVI.continuity.N.png                 test.spectra-cn.fl.png
test.athal_COL.cvi0.hapmer.wig                  test.athal_CVI.cvi0.hapmer.spectra-cn.fl.png    test.spectra-cn.hist
test.athal_COL.only.hist                        test.athal_CVI.cvi0.hapmer.spectra-cn.ln.png    test.spectra-cn.ln.png
test.athal_COL.qv                               test.athal_CVI.cvi0.hapmer.spectra-cn.st.png    test.spectra-cn.st.png
test.athal_COL.sort.bed                         test.athal_CVI.cvi0.hapmer.spectra-hap-cn.hist
[user@cn3144]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf]$

Create a batch input file (e.g. merqury.sh), which uses the test data in $MERQURY_TEST_DATA. For example:

#!/bin/bash
module load merqury/1.3
cp ${MERQURY_TEST_DATA:-none}/* .
for f in *.tar.gz ; do tar -xzf $f ; done
merqury.sh F1.k18.meryl col0.hapmer.meryl cvi0.hapmer.meryl athal_COL.fasta athal_CVI.fasta test

Submit this job using the Slurm sbatch command.

sbatch --cpus-per-task=6 --mem=10g merqury.sh