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Removing reads mapping to the lambda genome

Project description

# NanoLyse
Remove reads mapping to the lambda phage genome from a fastq file.
This script uses Heng Li's [minimap2]( and his [mappy]( Python binding.

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`pip install NanoLyse`

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.
Specify a reference fasta file against which to filter.

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

`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.

If you use this tool, please consider citing our [publication](

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