Package Recipe 'fjord'

recipe fjord

ONT amplicon sequencing pipeline for bacterial identification

Homepage:: https://github.com/adnsvrtsn/fjord
License:: MIT / MIT
Recipe:: /fjord/meta.yaml

FJORD (Flexible Joint Operational pipeline for Reference-based Diagnostics) is an amplicon sequencing pipeline for bacterial identification from Oxford Nanopore Technologies long-read data. It maps reads to a GTDB-formatted reference database, generates consensus sequences, clusters similar sequences with IUPAC-aware consolidation, and assigns taxonomy via BLAST.

package fjord¶

Versions:

1.0.0-0

Depends:

on bash >=3.2
on biopython
on blast
on python >=3.8
on samtools >=1.15
on vsearch
on x-mapper

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 fjord

to add into an existing workspace instead, run:

pixi add fjord

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 fjord

Alternatively, to install into a new environment, run:

conda create -n envname fjord

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/fjord:<tag>

(see fjord/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:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/fjord/README.html)