Lyveset

Introduction

Lyveset is a method of using hqSNPs to create a phylogeny, especially for outbreak investigations.

For more information, please check:
Docker hub: https://hub.docker.com/r/staphb/lyveset
Home page: https://github.com/lskatz/lyve-SET

Versions

  • 2.0.1

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

Module

You can load the modules by:

module load biocontainers
module load lyveset

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 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