squeezemeta
Link to section 'Introduction' of 'squeezemeta' Introduction
SqueezeMeta is a fully automated metagenomics pipeline, from reads to bins.
Home page: https://github.com/jtamames/SqueezeMeta
Link to section 'Versions' of 'squeezemeta' Versions
- 1.5.1
Link to section 'Commands' of 'squeezemeta' 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
Link to section 'Module' of 'squeezemeta' Module
You can load the modules by:
module load biocontainers
module load squeezemeta
Link to section 'Example job' of 'squeezemeta' Example job
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