Purdue University

pomoxis

Link to section 'Introduction' of 'pomoxis' Introduction

Pomoxis comprises a set of basic bioinformatic tools tailored to nanopore sequencing. Notably tools are included for generating and analyzing draft assemblies. Many of these tools are used by the research data analysis group at Oxford Nanopore Technologies.

Docker hub: https://hub.docker.com/r/zeunas/pomoxis
Home page: https://github.com/nanoporetech/pomoxis

Link to section 'Versions' of 'pomoxis' Versions

• 0.3.9

Link to section 'Commands' of 'pomoxis' 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

Link to section 'Module' of 'pomoxis' Module

You can load the modules by:

module load biocontainers
module load pomoxis

Link to section 'Example job' of 'pomoxis' Example job

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