sarek
rare-disease-wf
sarek | rare-disease-wf | |
---|---|---|
5 | 1 | |
338 | 56 | |
2.1% | - | |
9.9 | 0.0 | |
5 days ago | about 1 year ago | |
Nextflow | Nextflow | |
MIT License | MIT License |
Stars - the number of stars that a project has on GitHub. Growth - month over month growth in stars.
Activity is a relative number indicating how actively a project is being developed. Recent commits have higher weight than older ones.
For example, an activity of 9.0 indicates that a project is amongst the top 10% of the most actively developed projects that we are tracking.
sarek
- Recommendations for software or online resources
- Best somatic variant callers?
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GATK4 automated pipelines in existence?
The sarek pipeline from nf-core might interest you
- Workflow Question
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aws batch keeps the "Desired vCPUs" high long after they should be reduced
The issue is specific to https://github.com/nf-core/sarek and/or it's usage of https://www.nextflow.io/
rare-disease-wf
-
Ask HN: How to be my own genetic disease researcher for my partner?
Feel free to reach out, username at berkeley edu.
In open source bioinformatics we strive for reproducible science, which can be difficult in a field with tons of different methods and tools. One approach is to use a workflow language such as Nextflow [0] and Docker/Singularity such that the entire analysis is reproducible, see e.g. [1].
There is a vibrant community around Nextflow workflows called nf-core [2] which has a rare disease workflow in development [3], come join our slack!
[0] - https://nextflow.io
[1] - https://github.com/brentp/rare-disease-wf
[2] - https://nf-co.re
[3] - https://nf-co.re/raredisease
What are some alternatives?
GATK - Germline Variant Calling Nextflow Pipeline Based On GATK4 Best Practices
slivar - genetic variant expressions, annotation, and filtering for great good.
galaxy - Data intensive science for everyone.
gnomad-browser - Explore gnomAD datasets on the web
rnaseq-nf - A proof of concept of RNAseq pipeline
octopus - Bayesian haplotype-based mutation calling
mag - Assembly and binning of metagenomes
rnatoy - A proof of concept RNA-Seq pipeline with Nextflow
Exomiser - A Tool to Annotate and Prioritize Exome Variants
configs - Config files used to define parameters specific to compute environments at different Institutions
hlatyping - Precision HLA typing from next-generation sequencing data