GATK VS sarek

Compare GATK vs sarek and see what are their differences.

GATK

Germline Variant Calling Nextflow Pipeline Based On GATK4 Best Practices (by lifebit-ai)
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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
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nf-co.re
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GATK sarek
1 5
11 338
- 2.1%
10.0 9.9
about 4 years ago 6 days ago
Nextflow Nextflow
- MIT License
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GATK

Posts with mentions or reviews of GATK. We have used some of these posts to build our list of alternatives and similar projects. The last one was on 2022-03-11.
  • GATK4 automated pipelines in existence?
    2 projects | /r/bioinformatics | 11 Mar 2022
    Are you looking for a germline variant calling pipeline? If so, try https://github.com/lifebit-ai/GATK. If you know Nextflow, you can edit the script. Apparently, it uses Docker so you get the containerization.

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.

What are some alternatives?

When comparing GATK and sarek you can also consider the following projects:

galaxy - Data intensive science for everyone.

rnaseq-nf - A proof of concept of RNAseq pipeline

mag - Assembly and binning of metagenomes

rnatoy - A proof of concept RNA-Seq pipeline with Nextflow

configs - Config files used to define parameters specific to compute environments at different Institutions

patterns - A curated collection of Nextflow implementation patterns

eager - A fully reproducible and state-of-the-art ancient DNA analysis pipeline

rnaseq - RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.

rare-disease-wf - (WIP) best-practices workflow for rare disease

hlatyping - Precision HLA typing from next-generation sequencing data

CancerDB - CancerDB: a computable encyclopedia about cancer.

sarek vs galaxy sarek vs rnaseq-nf sarek vs mag sarek vs rnatoy sarek vs configs sarek vs patterns sarek vs eager sarek vs rnaseq sarek vs rare-disease-wf sarek vs hlatyping sarek vs CancerDB