recipe circleseeker

Comprehensive eccDNA detection from PacBio HiFi sequencing data with dual-engine support

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: - Dual-engine support: Cresil (preferred) and Cyrcular (fallback) with intelligent auto-selection - 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:

1.0.0-0

depends bcftools:

depends biopython:

>=1.81

depends cd-hit:

depends click:

>=8.1

depends cyrcular:

depends intervaltree:

>=3.1

depends last:

depends minimap2:

depends networkx:

>=3.0

depends numpy:

>=1.23

depends packaging:

>=23

depends pandas:

>=2.0

depends pysam:

>=0.22

depends python:

>=3.9

depends pyyaml:

>=6.0

depends samtools:

depends tidehunter:

depends varlociraptor:

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 circleseeker

and update with::

   mamba update circleseeker

To create a new environment, run:

mamba create --name myenvname circleseeker

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/circleseeker:<tag>

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

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