NanoLyse
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.
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.
WARNING
If (some of) the reads of your genome of interest are sufficiently similar to the lambda genome those reads will be lost.
EXAMPLES
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.
CITATION
If you use this tool, please consider citing our publication.
1 maintainer
Metadata
1 maintainer
Release files for NanoLyse 1.2.1
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| NanoLyse-1.2.1.tar.gz | 36.2 kB | Details |
Release files / NanoLyse-1.2.1.tar.gz
| Download URL | NanoLyse-1.2.1.tar.gz |
|---|---|
| Size | 36.2 kB |
| Tags | Source |
|
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