./wip/nanolyse, Removing reads mapping to the lambda genome

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Branch: CURRENT, Version:, Package name: NanoLyse-, Maintainer: pkgsrc-users

Remove reads mapping to the lambda phage genome from a fastq file.
This script uses Heng Li's minimap2 (https://github.com/lh3/minimap2)
and his mappy Python binding (https://pypi.python.org/pypi/mappy).

### 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 (https://github.com/wdecoster/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

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