recipe sabre

A barcode demultiplexing and trimming tool for FastQ files

Homepage:

https://github.com/najoshi/sabre/

License:

MIT

Recipe:

/sabre/meta.yaml

Next-generation sequencing can currently produce hundreds of millions of reads per lane of sample and that number increases at a dizzying rate. Barcoding individual sequences for multiple lines or multiple species is a cost-efficient method to sequence and analyze a broad range of data. Sabre is a tool that will demultiplex barcoded reads into separate files. It will work on both single-end and paired-end data in fastq format. It simply compares the provided barcodes with each read and separates the read into its appropriate barcode file, after stripping the barcode from the read (and also stripping the quality values of the barcode bases). If a read does not have a recognized barcode, then it is put into the unknown file. Sabre also has an option (-m) to allow mismatches of the barcodes. Sabre also supports gzipped file inputs. Also, since sabre does not use the quality values in any way, it can be used on fasta data that is converted to fastq by creating fake quality values. Finally, after demultiplexing, sabre outputs a summary of how many records went into each barcode file.

package sabre

(downloads) docker_sabre

Versions:

1.000-6,  1.000-5,  1.000-4,  1.000-3,  1.000-2,  1.000-1,  1.000-0

Depends:

  • on libgcc >=13

  • on libzlib >=1.3.1,<2.0a0

  • on zlib

Additional platforms:

Installation

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install sabre

to add into an existing workspace instead, run:

pixi add sabre

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install sabre

Alternatively, to install into a new environment, run:

conda create -n envname sabre

with envname being the name of the desired environment.

Container

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

docker pull quay.io/biocontainers/sabre:<tag>

(see sabre/tags for valid values for <tag>).

Integrated deployment

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

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