Cactus

Introduction

Cactus is a reference-free whole-genome multiple alignment program.

For more information, please check its website: https://biocontainers.pro/tools/cactus and its home page on Github.

Versions

  • 2.0.5

  • 2.2.1

Commands

  • cactus

  • cactus-align

  • cactus-align-batch

  • cactus-blast

  • cactus-graphmap

  • cactus-graphmap-join

  • cactus-graphmap-split

  • cactus-minigraph

  • cactus-prepare

  • cactus-prepare-toil

  • cactus-preprocess

  • cactus-refmap

  • cactus2hal-stitch.sh

  • cactus2hal.py

  • cactusAPITests

  • cactus_analyseAssembly

  • cactus_barTests

  • cactus_batch_mergeChunks

  • cactus_chain

  • cactus_consolidated

  • cactus_covered_intervals

  • cactus_fasta_fragments.py

  • cactus_fasta_softmask_intervals.py

  • cactus_filterSmallFastaSequences.py

  • cactus_halGeneratorTests

  • cactus_local_alignment.py

  • cactus_makeAlphaNumericHeaders.py

  • cactus_softmask2hardmask

Module

You can load the modules by:

module load biocontainers
module load cactus

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 Cactus on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=cactus
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers cactus

wget https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/master/examples/evolverMammals.txt
cactus jobStore evolverMammals.txt evolverMammals.hal