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Removing reads mapping to the lambda genome

Project description

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

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