Top 7 Nextflow Pipeline Projects
RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.Project mention: How to get NGS programming experience? | reddit.com/r/bioinformatics | 2023-01-31
I would suggest the nf-core/rnaseq pipeline. It's used by many core facilities around the world. Also, there are many more pipelines from nf-core, e.g. Sarek for variant calling.
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
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ChIP-seq peak-calling, QC and differential analysis pipeline.Project mention: Nextflow issue | reddit.com/r/bioinformatics | 2022-11-30
Launching https://github.com/nf-core/chipseq [pensive_euler] DSL2 - revision: 51eba00b32 [master]
ATAC-seq peak-calling, QC and differential analysis pipelineProject mention: Software repository and hackathons | reddit.com/r/longevity | 2022-06-29
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.
A fully reproducible and state-of-the-art ancient DNA analysis pipeline
Precision HLA typing from next-generation sequencing data
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Nextflow Pipeline related posts
GATK4 automated pipelines in existence?
2 projects | reddit.com/r/bioinformatics | 11 Mar 2022
Generate consensus FASTA files pipeline
1 project | reddit.com/r/ngs | 14 Jul 2021
1 project | reddit.com/r/bioinformatics | 9 Jul 2021
aws batch keeps the "Desired vCPUs" high long after they should be reduced
1 project | reddit.com/r/aws | 15 Mar 2021
What are some of the best open-source Pipeline projects in Nextflow? This list will help you: