A flexible read processor, capable of performing powerful transformations on your FASTA/FASTQ/BAM files.
You could use matchbox for:
- Quick, error-tolerant search for primers and known sequences
- Demultiplexing even the most complex barcoding schemes
- Investigating and filtering out sequencing artefacts
Read the documentation site for more examples, or check out the preprint.
matchbox can be installed using cargo:
cargo install matchbox-cliWrite your matchbox script in a .mb file, and give it to matchbox via --script.
matchbox -s my_script.mb my_reads.fq- To allow for edit distance when searching for sequences, use
--error - To process data on multiple threads for improved speed, use
--threads - To handle paired reads, use
--paired-with
For examples and a full scripting language reference, read the documentation!
If you use matchbox, cite the preprint at DOI:10.1101/2025.11.09.685711