recipe ngsep

NGSEP - Next Generation Sequencing Experience Platform

Homepage:

https://github.com/NGSEP/NGSEPcore

License:

GPL / GPL-3

Recipe:

/ngsep/meta.yaml

Links:

biotools: ngsep, doi: 10.1093/bioinformatics/btz275

NGSEP provides an object model to enable different kinds of analysis of DNA high throughput sequencing (HTS) data. The classic use of NGSEP is a reference guided construction and downstream analysis of large datasets of genomic variation. NGSEP performs accurate detection and genotyping of Single Nucleotide Variants (SNVs), small and large indels, short tandem repeats (STRs), inversions, and Copy Number Variants (CNVs). NGSEP also provides utilities for downstream analysis of variation in VCF files, including functional annotation of variants, filtering, format conversion, comparison, clustering, imputation, introgression analysis and different kinds of statistics.

package ngsep

(downloads) docker_ngsep

Versions:

4.0.1-0

Depends:

  • on openjdk >=8

  • 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 ngsep

to add into an existing workspace instead, run:

pixi add ngsep

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 ngsep

Alternatively, to install into a new environment, run:

conda create -n envname ngsep

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/ngsep:<tag>

(see ngsep/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.

Notes

Version 4 includes new modules for read alignment and de-novo analysis of short and long reads including calculations of k-mers, error correction, de-novo analysis of Genotype-by-sequencing data and (coming soon) de-novo assembly of long read whole genome sequencing (WGS) data.

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