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