Squeezemeta

Introduction

SqueezeMeta is a fully automated metagenomics pipeline, from reads to bins.

For more information, please check:
Home page: https://github.com/jtamames/SqueezeMeta

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