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.
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.
-r REFERENCE, --reference REFERENCE
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.