lyveset
Link to section 'Introduction' of 'lyveset' Introduction
Lyveset is a method of using hqSNPs to create a phylogeny, especially for outbreak investigations.
Docker hub: https://hub.docker.com/r/staphb/lyveset
Home page: https://github.com/lskatz/lyve-SET
Link to section 'Versions' of 'lyveset' Versions
- 2.0.1
Link to section 'Commands' of 'lyveset' Commands
- applyFstToTree.pl
- cladeDistancesFromTree.pl
- clusterPairwise.pl
- convertAlignment.pl
- downloadDataset.pl
- errorProneRegions.pl
- filterMatrix.pl
- filterVcf.pl
- genomeDist.pl
- launch_bwa.pl
- launch_set.pl
- launch_smalt.pl
- launch_snap.pl
- launch_snpeff.pl
- launch_varscan.pl
- makeRegions.pl
- matrixToAlignment.pl
- pairwiseDistances.pl
- pairwiseTo2d.pl
- removeUninformativeSites.pl
- removeUninformativeSitesFromMatrix.pl
- run_assembly_isFastqPE.pl
- run_assembly_metrics.pl
- run_assembly_readMetrics.pl
- run_assembly_removeDuplicateReads.pl
- run_assembly_shuffleReads.pl
- run_assembly_trimClean.pl
- set_bayesHammer.pl
- set_diagnose.pl
- set_diagnose_msa.pl
- set_downloadTestData.pl
- set_findCliffs.pl
- set_findPhages.pl
- set_indexCase.pl
- set_manage.pl
- set_processPooledVcf.pl
- set_samtools_depth.pl
- set_test.pl
- shuffleSplitReads.pl
- snpDistribution.pl
- vcfToAlignment.pl
- vcfutils.pl
Link to section 'Module' of 'lyveset' Module
You can load the modules by:
module load biocontainers
module load lyveset
Link to section 'Example job' of 'lyveset' 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 lyveset on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=lyveset
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers lyveset
set_test.pl lambda
set_manage.pl --create setTest