gatk4-genome-processing-pipeline-azure
Workflows used for processing whole genome sequence data + germline variant calling. (by microsoft)
juicer
A One-Click System for Analyzing Loop-Resolution Hi-C Experiments (by aidenlab)
| gatk4-genome-processing-pipeline-azure | juicer | |
|---|---|---|
| 4 | 1 | |
| 7 | 390 | |
| - | 3.8% | |
| 0.0 | 0.0 | |
| 2 months ago | 3 months ago | |
| wdl | Shell | |
| BSD 3-clause "New" or "Revised" 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.
gatk4-genome-processing-pipeline-azure
Posts with mentions or reviews of gatk4-genome-processing-pipeline-azure.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2023-04-05.
- What are some good examples of well-engineered bioinformatics pipelines?
-
Do you know how to get CNVs out of WES data sorted.bam files? (Free)
The GATK suite is pretty standard for calling germline mutations. Somatic mutation calling is a lot newer/trickier, so I'm just going to link to the GDC's practices.
-
Best way to document tool?
This pre-processing pipeline from Microsoft (adapted from the Broad Institute/GATK) is pretty well-documented - at least in my opinion - with input requirements, expected outputs, software requirements, etc.
juicer
Posts with mentions or reviews of juicer.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2023-04-05.
What are some alternatives?
When comparing gatk4-genome-processing-pipeline-azure and juicer you can also consider the following projects:
sv-callers - Snakemake-based workflow for detecting structural variants in genomic data
sage - Proteomics search & quantification so fast that it feels like magic
seqkit - A cross-platform and ultrafast toolkit for FASTA/Q file manipulation
veba - A modular end-to-end suite for in silico recovery, clustering, and analysis of prokaryotic, microeukaryotic, and viral genomes from metagenomes
rnaseq - RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
smk-simple-slurm - A simple Snakemake profile for Slurm without --cluster-config
spades - SPAdes Genome Assembler
trinityrnaseq - Trinity RNA-Seq de novo transcriptome assembly
gatk4-genome-processing-pipeline-azure vs sv-callers
juicer vs sage
gatk4-genome-processing-pipeline-azure vs sage
juicer vs seqkit
gatk4-genome-processing-pipeline-azure vs veba
juicer vs rnaseq
gatk4-genome-processing-pipeline-azure vs rnaseq
juicer vs smk-simple-slurm
gatk4-genome-processing-pipeline-azure vs seqkit
juicer vs spades
gatk4-genome-processing-pipeline-azure vs spades
juicer vs trinityrnaseq