slivar
rare-disease-wf
| slivar | rare-disease-wf | |
|---|---|---|
| 1 | 1 | |
| 241 | 56 | |
| - | - | |
| 5.7 | 0.0 | |
| 5 months ago | about 1 year ago | |
| Nim | 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.
slivar
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Help on installation of GEMINi
Looks like they’ve broken the install at some point. If you check the GitHub for Gemini it recommends you replace it with slivar https://github.com/brentp/slivar
rare-disease-wf
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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?
minimap2 - A versatile pairwise aligner for genomic and spliced nucleotide sequences
sarek - Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
deepvariant - DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
gnomad-browser - Explore gnomAD datasets on the web
bwa - Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)
octopus - Bayesian haplotype-based mutation calling
open-cravat - A modular annotation tool for genomic variants
rnaseq-nf - A proof of concept of RNAseq pipeline
Biopython - Official git repository for Biopython (originally converted from CVS)
Exomiser - A Tool to Annotate and Prioritize Exome Variants
codeql - GitHub Satellite 2020 workshops on finding security vulnerabilities with CodeQL for Java/JavaScript.
hlatyping - Precision HLA typing from next-generation sequencing data