NanoLyse 0.4.0

Removing reads mapping to the lambda genome

Remove reads mapping to the lambda phage genome from a fastq file.

This script uses Heng Li’s minimap2 and his mappy Python binding.

INSTALLATION

pip install NanoLyse

USAGE

Reads fastq from stdin and writes to stdout.

NanoLyse [-h] [-v] [-r REFERENCE]

                    Remove reads mapping to the lambda genome.
                    Reads fastq from stdin and writes to stdout.

                    Example usage:
                    zcat reads.fastq.gz | NanoLyse | gzip > reads_without_lambda.fastq.gz


optional arguments:
  -h, --help            show this help message and exit
  -v, --version         Print version and exit.
  -r REFERENCE, --reference REFERENCE
                        Specify a reference fasta file against which to filter.

WARNING

If (some of) the reads of your genome of interest are sufficiently similar to the lambda genome those reads will be lost.

EXAMPLES

gunzip -c reads.fastq.gz | NanoLyse | gzip > reads_without_lambda.fastq.gz

In combination with NanoFilt:

gunzip -c reads.fastq.gz | NanoLyse | NanoFilt -q 12 | gzip > filtered_reads_without_lambda.fastq.gz

Using a different genome to filter on (rather than lambda phage):

gunzip -c reads.fastq.gz | NanoLyse --reference mygenome.fa.gz | gzip > reads_without_mygenome.fastq.gz

I welcome all suggestions, bug reports, feature requests and contributions. Please leave an issue or open a pull request. I will usually respond within a day, or rarely within a few days.