octopus
rare-disease-wf
| octopus | rare-disease-wf | |
|---|---|---|
| 1 | 1 | |
| 296 | 56 | |
| 0.3% | - | |
| 4.0 | 0.0 | |
| 9 months ago | about 1 year ago | |
| C++ | 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.
octopus
-
genotyping tool
Check out octopus https://github.com/luntergroup/octopus
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?
megahit - Ultra-fast and memory-efficient (meta-)genome assembler
slivar - genetic variant expressions, annotation, and filtering for great good.
TileDB-VCF - Efficient variant-call data storage and retrieval library using the TileDB storage library.
sarek - Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
gnomad-browser - Explore gnomAD datasets on the web
rnaseq-nf - A proof of concept of RNAseq pipeline
Exomiser - A Tool to Annotate and Prioritize Exome Variants
hlatyping - Precision HLA typing from next-generation sequencing data