- recipe cfdna-biomarkersearch
Pipeline to identify candidate cfDNA biomarker sequences from WGS data
- Homepage:
- Documentation:
https://github.com/avo-hcemm/cfDNA-biomarkers-pipeline/blob/master/README.md
- License:
MIT / MIT
- Recipe:
cfDNA-BiomarkerDiscovery is a pipeline designed to identify candidate biomarker sequences from cell-free DNA (cfDNA) derived from blood samples. The pipeline takes as input: • An archive of FASTQ files containing paired-end reads from whole-genome sequencing (WGS) of one or more case cohorts and a control cohort. • Additional required files: adapter sequences, genome version for download, genome information file, parameter file, and an archive with genome FASTA files. The pipeline performs: 1. Preprocessing: adapter trimming, quality filtering, and alignment to the reference genome. 2. Analysis: identification of candidate genomic regions as potential biomarkers. If informative regions are identified, the pipeline generates a CSV file listing the candidate biomarker sequences along with their associated genomic coordinates.
- package cfdna-biomarkersearch¶
- Versions:
0.1.3-0,0.1.1-0- Depends:
on bowtie2
on ca-certificates
on curl
on fastqc
on gnupg
on imbalanced-learn
on multiqc
on numpy
on openjdk
>=21on pandas
on samtools
on scikit-bio
on scipy
on setuptools
<81on sklearn-compat
on tar
on trimmomatic
on unzip
on wget
on xgboost
- 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 cfdna-biomarkersearch
to add into an existing workspace instead, run:
pixi add cfdna-biomarkersearch
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 cfdna-biomarkersearch
Alternatively, to install into a new environment, run:
conda create -n envname cfdna-biomarkersearch
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/cfdna-biomarkersearch:<tag>
(see cfdna-biomarkersearch/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:
[](http://bioconda.github.io/recipes/cfdna-biomarkersearch/README.html)
