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

WARNING

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

Project links

Key dates

PyPI data
Data sourced directly from PyPI's database.
  • Released:
Newer release available (1.2.1)

1 maintainer

PyPI data
Data sourced directly from PyPI's database.
Avatar for wdecoster from gravatar.com wdecoster

Credits

Author: Wouter De Coster

License

MIT License (MIT)

Tags

nanopore sequencing processing

Classifiers

Report project as malware

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