recipe spliced_bam2gff

A tool to convert spliced BAM alignments into GFF2 format

Homepage:

https://github.com/nanoporetech/spliced_bam2gff

License:

MOZILLA / MPL-2

Recipe:

/spliced_bam2gff/meta.yaml

The spliced_bam2gff tool converts BAM alignments, produced by spliced aligners (such as minimap2, gmap), into a GFF2 format.

By default, introns are created based on the N cigar feature. Alternatively, if -d (i.e. for deletion) is specified, any deletions larger than the limit will be classified as an intron. The orientation of the GFF2 features is determined by the XS strand tag and SAM flags depending on the aligner.

The tool supports splitting the output into loci and bundles of loci with a minimum number of features, which enables easy parallelisation of downstream analyses.

package spliced_bam2gff

(downloads) docker_spliced_bam2gff

versions:

1.3-1,  1.3-0,  1.2-0

requirements:

Installation

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 spliced_bam2gff

and update with::

   mamba update spliced_bam2gff

To create a new environment, run:

mamba create --name myenvname spliced_bam2gff

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 quay.io/biocontainers/spliced_bam2gff:<tag>

(see `spliced_bam2gff/tags`_ for valid values for ``<tag>``)

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