A flexible read processor, capable of performing powerful transformations on your FASTA/FASTQ/SAM files.

You could use matchbox for:

• Quick, error-tolerant searches for primers and known sequences
• Validating the structure of your reads
• Quantifying and filtering out sequencing artefacts
• Demultiplexing even the most complex barcoding schemes

Read the documentation

Installation

matchbox can be installed using cargo:

cargo install matchbox-cli

Usage

Write 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!