Pomoxis

Introduction

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

For more information, please check:
Docker hub: https://hub.docker.com/r/zeunas/pomoxis
Home page: https://github.com/nanoporetech/pomoxis

Versions

  • 0.3.9

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

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 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