- recipe spliced_bam2gff
A tool to convert spliced BAM alignments into GFF2 format
- Homepage:
- License:
MOZILLA / MPL-2
- Recipe:
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¶
- Versions:
1.3-1,1.3-0,1.2-0- 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 spliced_bam2gff
to add into an existing workspace instead, run:
pixi add spliced_bam2gff
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 spliced_bam2gff
Alternatively, to install into a new environment, run:
conda create -n envname spliced_bam2gff
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/spliced_bam2gff:<tag>
(see spliced_bam2gff/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.
Download stats¶
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/spliced_bam2gff/README.html)
