gatk4-genome-processing-pipeline-azure
Workflows used for processing whole genome sequence data + germline variant calling. (by microsoft)
veba
A modular end-to-end suite for in silico recovery, clustering, and analysis of prokaryotic, microeukaryotic, and viral genomes from metagenomes (by jolespin)
| gatk4-genome-processing-pipeline-azure | veba | |
|---|---|---|
| 4 | 3 | |
| 7 | 57 | |
| - | - | |
| 0.0 | 8.7 | |
| 2 months ago | 6 days ago | |
| wdl | Python | |
| BSD 3-clause "New" or "Revised" License | GNU Affero General Public License v3.0 |
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?
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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.
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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.
veba
Posts with mentions or reviews of veba.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2022-11-01.
- Best way to document tool?
-
Is it ok to merge metagenome assemblies from two different assemblers?
Check out slides 7-10 here (I just made a presentation describing this). If that doesn't help, please skim through Astrobio Mike's blog post because it describes it in more detail.
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VEBA: a modular end-to-end suite for in silico recovery, clustering, and analysis of prokaryotic, microeukaryotic, and viral genomes from metagenomes (My most meaningful contribution to science thus far)
If you think this would be helpful for your research, give it a try (https://github.com/jolespin/veba)! If you have any trouble installing, let me know and I will gladly help debug; though, I've tested it several times. Currently, there's documentation on installation, modules, walkthroughs of workflows, and frequently asked questions.
What are some alternatives?
When comparing gatk4-genome-processing-pipeline-azure and veba you can also consider the following projects:
juicer - A One-Click System for Analyzing Loop-Resolution Hi-C Experiments
sv-callers - Snakemake-based workflow for detecting structural variants in genomic data
sage - Proteomics search & quantification so fast that it feels like magic
rnaseq - RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
seqkit - A cross-platform and ultrafast toolkit for FASTA/Q file manipulation
spades - SPAdes Genome Assembler