Skip to main content

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.


pip install NanoLyse


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 > filtered_reads_without_mygenome.fastq.gz


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


Build Status Code Health

Twitter URL

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-0.2.0.tar.gz (19.1 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