About

With next-generation sequencing tools capabilities, millions to billions of reads are generated. To reach such a rate in a cost-efficient manner, barcoding individual sequences for multiple lines or species is a common practice.

Sabreur is a tool that aims to demultiplex barcoded reads into separate files. It supports both fasta and fastq files. Input files can be gzip, bzip2 or xz compressed in input or output (Thanks to the awesome niffler crate). If an uncompressed file is provided the output is by default uncompressed. But this behaviour can be changed by settingn the --format option to the desired compress format. The --format option if specified while input files are compressed changes output files to the specified compress format. Sabreur in its core compares the provided barcodes with each read, then separates the read into its appropriate file. If a read does not have a recognized barcode, then it is put into an unknown file.

How to use sabreur

Paired-end mode

sabreur barcode.txt input_R1.fq.gz input_R2.fq.gz

Single-end mode

sabreur barcode.txt input.fq

Input sequences files can be fasta or fastq, compressed or not. The supported compression format are gz, bz2, xz and zst. Just give the sequences, sabreur know how to handle it!

Command-line arguments

``` USAGE: sabreur [options] []

ARGS: input barcode file input forward fastx file input reverse fastx file

OPTIONS: -m, --mismatch maximum number of mismatches [default: 0] -o, --out