gatk4-data-processing
Workflows for processing high-throughput sequencing data for variant discovery with GATK4 and related tools (by gatk-workflows)
amazon-genomics-cli-demos
Demos of what can be done with the Amazon Genomics CLI (by aws-samples)
| gatk4-data-processing | amazon-genomics-cli-demos | |
|---|---|---|
| 1 | 1 | |
| 142 | 3 | |
| 4.9% | - | |
| 0.0 | 0.0 | |
| almost 2 years ago | about 2 years ago | |
| wdl | Jupyter Notebook | |
| BSD 3-clause "New" or "Revised" License | MIT No Attribution |
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-data-processing
Posts with mentions or reviews of gatk4-data-processing.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2022-04-26.
-
Profiling workflows with the Amazon Genomics CLI
To run a workflow with AGC you use commands like the following - in this case I’m running the GATK data processing workflow that is included as an example when you install AGC:
amazon-genomics-cli-demos
Posts with mentions or reviews of amazon-genomics-cli-demos.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2022-04-26.
-
Profiling workflows with the Amazon Genomics CLI
Importantly, the method above can be used for any workflow that AGC can run so you don’t have to remember engine specific details of how to get such profiling information. This opens up the possibility of comparing the performance a workflow across workflow engines, which is something I’ll explore further in a future blog post. In the meantime, I recommend generating some plots of your own! All the Python code I used above is available in Github.
What are some alternatives?
When comparing gatk4-data-processing and amazon-genomics-cli-demos you can also consider the following projects:
amazon-genomics-cli
full_spectrum_bioinformatics - An open-access bioinformatics text
jq - Command-line JSON processor [Moved to: https://github.com/jqlang/jq]
awscurl - curl-like access to AWS resources with AWS Signature Version 4 request signing.