Squeezemeta¶
Introduction¶
SqueezeMeta is a fully automated metagenomics pipeline, from reads to bins.
Versions¶
1.5.1
Commands¶
01.merge_assemblies.pl
01.merge_sequential.pl
01.remap.pl
01.run_assembly.pl
01.run_assembly_merged.pl
02.rnas.pl
03.run_prodigal.pl
04.rundiamond.pl
05.run_hmmer.pl
06.lca.pl
07.fun3assign.pl
08.blastx.pl
09.summarycontigs3.pl
10.mapsamples.pl
11.mcount.pl
12.funcover.pl
13.mergeannot2.pl
14.runbinning.pl
15.dastool.pl
16.addtax2.pl
17.checkM_batch.pl
18.getbins.pl
19.getcontigs.pl
20.minpath.pl
21.stats.pl
SqueezeMeta.pl
SqueezeMeta_conf.pl
SqueezeMeta_conf_original.pl
parameters.pl
restart.pl
add_database.pl
cover.pl
sqm2ipath.pl
sqm2itol.pl
sqm2keggplots.pl
sqm2pavian.pl
sqm_annot.pl
sqm_hmm_reads.pl
sqm_longreads.pl
sqm_mapper.pl
sqm_reads.pl
versionchange.pl
find_missing_markers.pl
remove_duplicate_markers.pl
anvi-filter-sqm.py
anvi-load-sqm.py
sqm2anvio.pl
configure_nodb.pl
configure_nodb_alt.pl
download_databases.pl
make_databases.pl
make_databases_alt.pl
test_install.pl
Module¶
You can load the modules by:
module load biocontainers
module load squeezemeta
Example job¶
Warning
Using #!/bin/sh -l
as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash
instead.
To run squeezemeta on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=squeezemeta
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers squeezemeta
SqueezeMeta.pl -m coassembly -p Hadza -s test.samples -f raw