Pomoxis Programs¶

Below you will find a listing with brief description of all the tools within pomoxis. For more information concerning each tool simply run it on the command line with the --help option.

More complex workflows (using tools from pomoxis) can be found within the katuali software package.

assess_assembly¶

Calculate accuracy statistics for an assembly.

assess_assembly [-h] -r <reference> -i <fastq>

assess_homopolymers¶

Analyse homopolymer query and reference lengths.

homopolymer [-h] {count,analyse} ...

catalogue_errors¶

Create a catalogue of all query errors in a bam.

catalogue_errors [-h] [--bed BED] [-t THREADS] [-o OUTDIR] bam

common_errors_from_bam¶

Get errors common to multiple assemblies aligned to ref.

common_errors_from_bam [-h] [-o OUTPUT_PREFIX] bam ref_fasta

coverage_from_bam¶

Calculate read coverage depth from a bam.

coverage_from_bam [-h] [-r REGIONS [REGIONS ...]]
                         [-p PREFIX | -o ONE_FILE] [-s STRIDE]
                         [--summary_only]
                         bam

coverage_from_fastx¶

Estimate coverage from summed basecall and reference lengths

coverage_from_fastx [-h] [--coverage COVERAGE] [--longest]
                           basecalls ref_len

fast_convert¶

Convert between fasta<->fastq.

fast_convert [-h] [--discard_q] [--mock_q MOCK_Q] {qq,aa,aq,qa}

find_indels¶

Parse a bamfile and document indels.

find_indels [-h] [-m MIN_INDEL_LENGTH] [-a] [-o OUTPUT] [-b BED]
                   [-t THREADS]
                   bam

intersect_assembly_errors¶

Assess errors which occur in the same reference position accross multiple assemblies.

intersect_assembly_errors [-h] -r <reference> -i <fasta>

long_fastx¶

Extract longest reads from a fastq.

long_fastx [-h] (--longest LONGEST | --bases BASES) [--others OTHERS]
                  input output

mini_align¶

Align fastq/a formatted reads to a genome using minimap2.

mini_align [-h] -r <reference> -i <fastq>

mini_assemble¶

Assemble fastq/fasta formatted reads and perform POA consensus.

mini_assemble [-h] -i <fastq>

pomoxis_path¶

Print the path of bundled executables.

pomoxis_path [-h] program

qscores_from_summary¶

Extract Q scores from summary_from_stats output

qscores_from_summary [-h] [--median] [--ref REF]
                            summaries [summaries ...]

ref_seqs_from_bam¶

Extract reference sequence that queries are aligned to

ref_seqs_from_bam [-h] bam

reverse_bed¶

Convert bed-file coordinates to coordinates on the reverse strand.

reverse_bed [-h] bed_in ref_fasta bed_out

split_fastx¶

Split records in a fasta/q file into chunks of a maximum size.

split_fastx [-h] input output chunksize

stats_from_bam¶

Parse a bamfile (from a stream) and output summary stats for each read.

stats_from_bam [-h] [--bed BED] [-m MIN_LENGTH] [-a] [-o OUTPUT]
                      [-s SUMMARY] [-t THREADS]
                      bam

subsample_bam¶

Subsample a bam to uniform or proportional depth

subsample_bam [-h] [-o OUTPUT_PREFIX] [-r REGIONS [REGIONS ...]]
                     [-p PROFILE] [-O {fwd,rev}] [-t THREADS] [-q QUALITY]
                     [-a ACCURACY] [-c COVERAGE] [-l LENGTH]
                     [--any_fail | --all_fail] [-x PATIENCE] [-s STRIDE] [-P]
                     [-S SEED]
                     bam depth [depth ...]

summary_from_stats¶

Summarise output of stats_from_bam.

summary_from_stats [-h] [-i INPUT] [-o OUTPUT]
                          [-p PERCENTILES [PERCENTILES ...]] [-pr]

tag_bam¶

Add a tag to all alignments in a bam.

tag_bam [-h] input output tag_name tag_value

trim_alignments¶

Trim alignments in multiple bams to common overlap window.

trim_alignments [-h] [-r REF_NAME] [-o OUTPUT_PREFIX]
                       [-f REFERENCE_FASTA]
                       bams [bams ...]