sarek
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing (by nf-core)
configs
Config files used to define parameters specific to compute environments at different Institutions (by nf-core)
Our great sponsors
| sarek | configs | |
|---|---|---|
| 5 | 1 | |
| 333 | 77 | |
| 4.2% | - | |
| 9.8 | 9.7 | |
| 1 day ago | 7 days 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.
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.
- Recommendations for software or online resources
- Best somatic variant callers?
-
GATK4 automated pipelines in existence?
The sarek pipeline from nf-core might interest you
- Workflow Question
-
aws batch keeps the "Desired vCPUs" high long after they should be reduced
The issue is specific to https://github.com/nf-core/sarek and/or it's usage of https://www.nextflow.io/
configs
Posts with mentions or reviews of configs.
We have used some of these posts to build our list of alternatives
and similar projects.
-
Why does it feels impossible to set up github nextflow pipeline without a root?
To pick a random example config file (https://github.com/nf-core/configs/blob/master/conf/cambridge.config) - they have specified that singularity should be used, that the cluster's job scheduler is slurm and the maximum memory/time/cpus.
What are some alternatives?
When comparing sarek and configs you can also consider the following projects:
GATK - Germline Variant Calling Nextflow Pipeline Based On GATK4 Best Practices
argo-events - Event-driven Automation Framework for Kubernetes
galaxy - Data intensive science for everyone.
rnaseq - RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
rnaseq-nf - A proof of concept of RNAseq pipeline
rnatoy - A proof of concept RNA-Seq pipeline with Nextflow
mag - Assembly and binning of metagenomes
patterns - A curated collection of Nextflow implementation patterns
eager - A fully reproducible and state-of-the-art ancient DNA analysis pipeline