- 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 bowtie2:
- depends ca-certificates:
- depends curl:
- depends fastqc:
- depends gnupg:
- depends imbalanced-learn:
- depends multiqc:
- depends numpy:
- depends openjdk:
>=21- depends pandas:
- depends samtools:
- depends scikit-bio:
- depends scipy:
- depends setuptools:
<81- depends sklearn-compat:
- depends tar:
- depends trimmomatic:
- depends unzip:
- depends wget:
- depends xgboost:
- 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 cfdna-biomarkersearch and update with:: mamba update cfdna-biomarkersearch
To create a new environment, run:
mamba create --name myenvname cfdna-biomarkersearch
with
myenvnamebeing 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/cfdna-biomarkersearch:<tag> (see `cfdna-biomarkersearch/tags`_ for valid values for ``<tag>``)
Download stats¶
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/cfdna-biomarkersearch/README.html)
