sarek VS rare-disease-wf

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

sarek

Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing (by nf-core)
nextflow Workflow Pipeline Bioinformatics Genomics cancer next-generation-sequencing Conda reproducible-research Containers germline somatic variant-calling nf-core gatk4 Annotation whole-genome-sequencing whole-exome-sequencing pre-processing target-panels
Source Code
nf-co.re
Suggest alternative
Edit details

rare-disease-wf

(WIP) best-practices workflow for rare disease (by brentp)
Variants rare-disease Genomics
Source Code
Suggest alternative
Edit details
InfluxDB - Power Real-Time Data Analytics at Scale
Get real-time insights from all types of time series data with InfluxDB. Ingest, query, and analyze billions of data points in real-time with unbounded cardinality.
www.influxdata.com
featured
SaaSHub - Software Alternatives and Reviews
SaaSHub helps you find the best software and product alternatives
www.saashub.com
featured
sarek rare-disease-wf
5 1
338 56
2.1% -
9.9 0.0
6 days ago about 1 year 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.

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.

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

What are some alternatives?

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

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

sarek vs GATK rare-disease-wf vs slivar sarek vs galaxy rare-disease-wf vs gnomad-browser sarek vs rnaseq-nf rare-disease-wf vs octopus sarek vs mag rare-disease-wf vs rnaseq-nf sarek vs rnatoy rare-disease-wf vs Exomiser sarek vs configs rare-disease-wf vs hlatyping