Please be aware that NanoLyse will no longer receive any updates, as its functionality is included in chopper (which should be lots faster, too).

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.