- recipe notramp
Super-fast Normalization and Trimming for Amplicon Sequencing Data (Long- and Short-read)
- Homepage:
- Documentation:
- License:
BSD / BSD-2
- Recipe:
NoTrAmp is a Tool for super fast trimming and read-depth normalization of amplicon reads. It is designed to be used in amplicon-tiling panels (or similar multiplexed amplicon sequencing approaches) to cap coverage of each amplicon (if desired) and to trim amplicons to their appropriate length removing barcodes, adpaters and primers (if desired) in a single clipping step.
NoTrAmp is suitable for use with both long (e.g. ONT/PacBio) and short reads (e.g Illumina). When using reads that are significantly shorter than amplicon sizes, you should adjust the minimum required alignment length using the --set_min_len argument.
See the projects [home](https://github.com/simakro/NoTrAmp) for usage and additional documentation.
- package notramp¶
- Versions:
1.1.9-0,1.1.8-0,1.1.7-0,1.1.6-1,1.1.6-0,1.0.5-0- Depends:
on minimap2
on psutil
on python
- 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 notramp
to add into an existing workspace instead, run:
pixi add notramp
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 notramp
Alternatively, to install into a new environment, run:
conda create -n envname notramp
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/notramp:<tag>
(see notramp/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/notramp/README.html)
