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.