Nextflow Annotation Projects
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencingProject mention: GATK4 automated pipelines in existence? | reddit.com/r/bioinformatics | 2022-03-11
The sarek pipeline from nf-core might interest you
Assembly and binning of metagenomesProject mention: How do you use Termux? | reddit.com/r/termux | 2022-07-16
So, I'm a bioinformatician, and currently I am extending my company's data processing pipeline which takes metagenomic sequencing data and performs a number of downstream analyses on it, the results of which are then provided to our customers. Here is an example of such a data processing pipeline: it's a script which orchestrates the execution of a number of tools to get the desired end result. Each of the green bubbles in the flowchart represents a single program which needs to be called specific settings and with data provided to it either by me (as the pipeline input) or from outputs of previous steps in the pipeline.
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