recipe wepp

Wastewater-Based Epidemiology using Phylogenetic Placements

Homepage:

https://github.com/TurakhiaLab/WEPP

Documentation:

https://turakhia.ucsd.edu/WEPP

License:

MIT / MIT

Recipe:

/wepp/meta.yaml

WEPP (Wastewater-Based Epidemiology using Phylogenetic Placements) is a pathogen-agnostic pipeline that enhances wastewater surveillance by leveraging the pathogen's full phylogeny. It reports haplotype and lineage abundances, maps reads parsimoniously to selected haplotypes, and flags Unaccounted Alleles — those observed in the sample but unexplained by selected haplotypes, potentially indicating novel variants. WEPP performs parsimonious read placement on the mutation-annotated tree (MAT) to select a subset of haplotypes and adds their neighbors to form an initial candidate pool, which is passed to a deconvolution algorithm to estimate their relative abundances. An interactive dashboard enables visualization of haplotypes in the global phylogenetic tree and read-level analysis.

package wepp

versions:

0.1.4.1-0

depends aiohttp:

depends altair:

depends biopython:

depends boost:

1.78.0.*

depends conda:

depends jsoncpp:

>=1.9.6,<1.9.7.0a0

depends libgcc:

>=13

depends libstdcxx:

>=13

depends mpich:

>=4.3.1,<5.0a0

depends nodejs:

>=20.12.2,<21.0a0

depends pandas:

depends pip:

depends protobuf:

<4

depends snakemake-minimal:

>=7.0

depends tbb:

>=2020.2,<2021.0.0a0

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 wepp

and update with::

   mamba update wepp

To create a new environment, run:

mamba create --name myenvname wepp

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/wepp:<tag>

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

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Render an badge with the following MarkDown:

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