Skip to main content

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.

[![Twitter URL](](
[![Build Status](]( [![Code Health](](
[![install with bioconda](](

`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](

Project details

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

NanoLyse-1.1.0.tar.gz (20.4 kB view hashes)

Uploaded Source

Supported by

AWS AWS Cloud computing and Security Sponsor Datadog Datadog Monitoring Fastly Fastly CDN Google Google Download Analytics Microsoft Microsoft PSF Sponsor Pingdom Pingdom Monitoring Sentry Sentry Error logging StatusPage StatusPage Status page