Package Recipe 'circleseeker'

recipe circleseeker

Comprehensive eccDNA detection from PacBio HiFi sequencing data

Homepage:: https://github.com/leoxqy/CircleSeeker
Documentation:: https://github.com/leoxqy/CircleSeeker#readme
License:: GPL / GPL-3.0-only
Recipe:: /circleseeker/meta.yaml

CircleSeeker is a specialized bioinformatics pipeline designed for the identification, classification, and characterization of extrachromosomal circular DNA (eccDNA) from PacBio HiFi long-read sequencing data.

Key features: - CtcReads-Core: TideHunter-based confirmed eccDNA detection - SplitReads-Core: Built-in split-read inference (HiFi optimized) - Hybrid detection strategy combining tandem repeat detection with split-read assembly - Comprehensive eccDNA classification (UeccDNA, MeccDNA, CeccDNA, XeccDNA) - Automated pipeline with checkpoint and resumption capabilities - Detailed HTML reports and comprehensive output formats - Modular architecture with 16 processing steps

package circleseeker¶

Versions:

1.1.1-0, 1.0.0-0

Depends:

on biopython >=1.81
on cd-hit
on click >=8.1
on intervaltree >=3.1
on last
on mappy >=2.26
on minimap2
on networkx >=3.0
on numpy >=1.23
on packaging >=23
on pandas >=2.0
on pybedtools >=0.9.0
on pysam >=0.22
on python >=3.9
on pyyaml >=6.0
on samtools
on tidehunter

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 circleseeker

to add into an existing workspace instead, run:

pixi add circleseeker

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 circleseeker

Alternatively, to install into a new environment, run:

conda create -n envname circleseeker

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/circleseeker:<tag>

(see circleseeker/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/circleseeker/README.html)