- recipe egap
EGAP pipeline for genome assembly and QC analysis
- Homepage:
- License:
BSD 3-Clause License
- Recipe:
EGAP (Entheome Genome Assembly Pipeline) is a versatile bioinformatics pipeline for hybrid genome assembly from Oxford Nanopore, Illumina, and PacBio data. It supports multiple input modes and assembly methods and determines the best based on multiple metrics: BUSCO Completeness (Single + Duplicated), Assembly Contig Count, Assembly N50, Assembly L50, and Assembly GC-content.
- package egap¶
- versions:
2.6.5-0,2.6.4-0,2.6.2-0,2.5.4-0,2.5.3-0- depends abyss:
>=2.0.2- depends bamtools:
>=2.5.2- depends bbmap:
>=39.15- depends beautifulsoup4:
>=4.12.3- depends bifrost:
>=1.3.5- depends biopython:
>=1.81- depends bwa:
>=0.7.18- depends compleasm:
>=0.2.6- depends fastqc:
>=0.12.1- depends flye:
>=2.9.5- depends gfatools:
>=0.5- depends hifiasm:
>=0.21.0- depends kmc:
>=3.2.4- depends masurca:
>=4.1.2- depends matplotlib-base:
>=3.7.3- depends minimap2:
>=2.28- depends nanoplot:
>=1.43.0- depends ncbi-datasets-cli:
>=16.39.0- depends pbccs:
>=6.4.0- depends pilon:
>=1.22- depends psutil:
>=6.0.0- depends purge_dups:
>=1.2.6- depends python:
>=3.8,<3.9- depends quast:
>=5.2.0- depends racon:
>=1.5.0- depends ragtag:
>=2.1.0- depends ratatosk:
>=0.9.0- depends samtools:
>=1.21- depends sepp:
>=4.5.1- depends spades:
>=4.0.0- depends sra-tools:
>=3.2.0- depends termcolor:
>=2.3.0- depends tgsgapcloser:
>=1.2.1- depends trimmomatic:
>=0.39- requirements:
- additional platforms:
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 egap and update with:: mamba update egap
To create a new environment, run:
mamba create --name myenvname egap
with
myenvnamebeing 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/egap:<tag> (see `egap/tags`_ for valid values for ``<tag>``)
Notes¶
This package installs a custom executable named "EGAP" in $PREFIX/bin. Please refer to the upstream GitHub page for usage instructions.
Download stats¶
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/egap/README.html)
