Pore_c_py

This package provides Python scripts for working with Pore-C data. It is not intended to be used directly by end uses, but rather as part of our Nextflow workflow wf-pore-c. Hence the terse nature of this documentation.

Installation

A package is available to install through either pip:

pip install pore-c-py

or through conda:

conda install -c nanoporetech pore-c-py

Usage

$ pore-c-py --help
usage: pore_c_py [OPTIONS] COMMAND [ARGS].

Available subcommands are:
    digest       Digest concatemer sequences into monomers using a restriction enzyme.      
    annotate     Annotate alignments with a "walk", which simply
                 enumerates the alignment coordinates of the monomers comprising the
                 concatemer.

Example

The following is indicative use, similar to that performed by wf-pore-c.

INPUT="myreads.bam"
ENZYME="NlaIII"
REF="myref.fasta"
OUTPUT="all"

pore-c-py digest "${INPUT}" "${ENZYME}" \
    | samtools fastq -T '*' \
    | minimap2 -ay -t 8 -x map-ont "${REF}" - \
    | pore-c-py annotate - "${OUTPUT}" --monomers --stdout --summary --chromunity \
    | tee "${OUTPUT}.ns.bam" \
    | samtools sort --write-index -o "${OUTPUT}.cs.bam" -
samtools index "${OUTPUT}.ns.bam"

The digest program can read its input from standard input, so it can be used with bamindex in order to process a subset of a file. This is particularly useful for distributing the workload on a cluster.