rare-disease-wf
(WIP) best-practices workflow for rare disease (by brentp)
sarek
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing (by nf-core)
Our great sponsors
| rare-disease-wf | sarek | |
|---|---|---|
| 1 | 5 | |
| 56 | 333 | |
| - | 4.2% | |
| 0.0 | 9.8 | |
| about 1 year ago | 5 days ago | |
| Nextflow | Nextflow | |
| MIT License | MIT License |
The number of mentions indicates the total number of mentions that we've tracked plus the number of user suggested alternatives.
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.
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.
rare-disease-wf
Posts with mentions or reviews of rare-disease-wf.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2021-12-06.
-
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
sarek
Posts with mentions or reviews of sarek.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2022-03-11.
- Recommendations for software or online resources
- Best somatic variant callers?
-
GATK4 automated pipelines in existence?
The sarek pipeline from nf-core might interest you
- Workflow Question
-
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/
What are some alternatives?
When comparing rare-disease-wf and sarek you can also consider the following projects:
slivar - genetic variant expressions, annotation, and filtering for great good.
GATK - Germline Variant Calling Nextflow Pipeline Based On GATK4 Best Practices