recipe barcode_splitter

Split multiple fastq files by matching barcodes in one or more of the sequence files. Barcodes in the tab-delimited barcodes.txt file are matched against the beginning (or end) of the specified index read(s). By default, barcodes must match exactly, but --mistmatches can be set higher if desired. Compressed input is read (from all files) if the first input file name ends in .gz. Reading of compressed input can be forced with the gzipin option.







doi: 10.5281/zenodo.2566616

package barcode_splitter

(downloads) docker_barcode_splitter



depends python:



You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install barcode_splitter

and update with::

   mamba update barcode_splitter

To create a new environment, run:

mamba create --name myenvname barcode_splitter

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull<tag>

(see `barcode_splitter/tags`_ for valid values for ``<tag>``)

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