Purdue University

Commands

• assess_assembly
• catalogue_errors
• common_errors_from_bam
• coverage_from_bam
• coverage_from_fastx
• fast_convert
• find_indels
• intersect_assembly_errors
• long_fastx
• mini_align
• mini_assemble
• pomoxis_path
• qscores_from_summary
• ref_seqs_from_bam
• reverse_bed
• split_fastx
• stats_from_bam
• subsample_bam
• summary_from_stats
• tag_bam
• trim_alignments

Module

You can load the modules by:

module load biocontainers
module load pomoxis

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 pomoxis on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 4
#SBATCH --job-name=pomoxis
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers pomoxis

assess_assembly \
    -i helen_output/Staph_Aur_draft_helen.fa \
    -r truth_assembly_staph_aur.fasta \
    -p polished_assembly_quality \
    -l 50 \
    -t 4 \
    -e \
    -T