Quick start

Welcome to the official user documentation for matchbox, a flexible processor for FASTA/FASTQ/SAM/BAM 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

Installation

Clone the GitHub repo and build it using cargo. More accessible distribution coming soon!

git clone https://github.com/jakob-schuster/matchbox.git
cd matchbox
cargo build --release

# then, run matchbox from the release directory
./target/release/matchbox --help

Command-line usage

matchbox takes in reads, in FASTA, FASTQ, SAM or BAM formats. If no file path is given, matchbox expects to receive reads from stdin.

matchbox also requires a configuration script, written in the matchbox scripting language as a .mb file. This script will tell matchbox how to process your reads.

matchbox -s my_script.mb reads.fq

Paired-end reads

If your reads are paired-end, the --paired-with parameter can be used.

matchbox -s my_script.mb read1.fq.gz --paired-with read2.fq.gz

Error tolerance

When performing pattern-matching, matchbox tolerates insertions, deletions and substitutions. The global error rate is used for all sequences.

# 15% error rate
matchbox -s my_script.mb reads.fq -e 0.15

# 0% error rate (only search for exact matches)
matchbox -s my_script.mb reads.fq -e 0