sabreur: fast, reliable and handy demultiplexing tool for fastx files.

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.fa --format xz

Input sequences files can be fasta or fastq, gzipped or not. Just give the sequences, sabreur know how to handle it!

Command-line arguments

``` USAGE: sabreur [FLAGS] [OPTIONS] [REVERSE]

FLAGS: --force Force reuse of output directory -h, --help Prints help information -q, --quiet Decrease program verbosity -V, --version Prints version information

OPTIONS: -f, --format Set output files compression format. [possible values: gz, xz, bz2] -l, --level Set the compression level [default: 1] [possible values: 1, 2, 3, 4, 5, 6, 7, 8, 9] -m, --mismatch Maximum number of mismatches allowed in a barcode [default: 0] -o, --out Output folder [default: sabreur_out]

ARGS: Input barcode file. Input forward fasta or fastq file. Can be gz, xz or bz2 compressed. Input reverse fasta or fastq file. Can be gz, xz or bz2 compressed. ```

Requirements

• Rust in stable channel
• libgz for gz file support
• liblzma for xz file support
• libbzip2 for bzip2 file support

Installation

From crates.io

If you already have a functional rust installation do:

cargo install sabreur

From source

``` git clone https://github.com/Ebedthan/sabreur.git cd sabreur

cargo build --release cargo test cargo install --path . ```

Benchmark

We used hyperfine for benchmarking with this dataset.

| Tool | Single-end uncompressed output | Single-end compressed output | Paired-end uncompressed output | Paired-end compressed output | | :--- | :----: | :----: | :----: | :----: | | idemp | - | 211.571 ± 3.718 | - | 366.247 ± 10.482 | | sabre | 32.911 ± 2.411 | - | 109.470 ± 49.909 | - | | sabreur | 10.843 ± 0.531| 93.840 ± 0.446 | 40.878 ± 13.743 | 187.533 ± 0.572 |

Note

Sabreur use a special barcode tab-delimited file format in the form:

barcode1 barcode1_file1.fq barcode1_file2.fq barcode2 barcode2_file1.fq barcode2_file2.fq ...

Contributions

Contributions are welcomed under the project code of conduct.

Bugs

Submit problems or requests to the Issue Tracker.

License

Licensed under the MIT license http://opensource.org/licenses/MIT. This project may not be copied, modified, or distributed except according to those terms.

Code of conduct

Please note that the sabreur project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.