NanoLyse 0.5.1

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.

Simple example:

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

WARNING

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

STATUS