rare-disease-wf VS octopus

Compare rare-disease-wf vs octopus and see what are their differences.

rare-disease-wf

(WIP) best-practices workflow for rare disease (by brentp)
Variants rare-disease Genomics
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octopus

Bayesian haplotype-based mutation calling (by luntergroup)
Genomics variant-calling Bioinformatics Variants haplotypes somatic-variants de-novo-mutation phasing single-cell
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rare-disease-wf octopus
1 1
56 296
- 1.4%
0.0 4.0
about 1 year ago 9 months ago
Nextflow C++
MIT License MIT License
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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?
    4 projects | news.ycombinator.com | 6 Dec 2021
    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

octopus

Posts with mentions or reviews of octopus. We have used some of these posts to build our list of alternatives and similar projects.

What are some alternatives?

When comparing rare-disease-wf and octopus you can also consider the following projects:

slivar - genetic variant expressions, annotation, and filtering for great good.

megahit - Ultra-fast and memory-efficient (meta-)genome assembler

sarek - Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing

TileDB-VCF - Efficient variant-call data storage and retrieval library using the TileDB storage library.

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

rare-disease-wf vs slivar octopus vs megahit rare-disease-wf vs sarek octopus vs TileDB-VCF rare-disease-wf vs gnomad-browser rare-disease-wf vs rnaseq-nf rare-disease-wf vs Exomiser rare-disease-wf vs hlatyping