Cactus

Introduction

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

Versions

• 2.8.1

• 2.8.1-gpu

Commands

• cactus

• cactus2hal.py

• cactus2hal-stitch.sh

• cactus-align

• cactus-align-batch

• cactus_analyseAssembly

• cactusAPITests

• cactus_barTests

• cactus_batch_mergeChunks

• cactus-blast

• cactus_chain

• cactus_consolidated

• cactus_covered_intervals

• cactus_fasta_fragments.py

• cactus_fasta_softmask_intervals.py

• cactus_filterSmallFastaSequences.py

• cactus-graphmap

• cactus-graphmap-join

• cactus-graphmap-split

• cactus_halGeneratorTests

• cactus_local_alignment.py

• cactus_makeAlphaNumericHeaders.py

• cactus-minigraph

• cactus-prepare

• cactus-prepare-toil

• cactus-preprocess

• cactus-refmap

• cactus_softmask2hardmask

Example job

Adjust slurm options based on job requirements (slurm cheat sheet):

#!/bin/bash
#SBATCH -p partitionName  # batch, gpu, preempt, mpi or your group's own partition
#SBATCH -t 1:00:00  # Runtime limit (D-HH:MM:SS)
#SBATCH -N 1   # Number of nodes
#SBATCH -n 1   # Number of tasks per node
#SBATCH -c 4   # Number of CPU cores per task
#SBATCH --mem=8G       # Memory required per node
#SBATCH --job-name=cactus      # Job name
#SBATCH --mail-type=FAIL,BEGIN,END     # Send an email when job fails, begins, and finishes
#SBATCH --mail-user=your.email@tufts.edu       # Email address for notifications
#SBATCH --error=%x-%J-%u.err   # Standard error file: <job_name>-<job_id>-<username>.err
#SBATCH --output=%x-%J-%u.out  # Standard output file: <job_name>-<job_id>-<username>.out

module purge   ### Optional, but highly recommended.
module load cactus/XXXX        ### Latest version is recommended.