covalent
sv-callers
| covalent | sv-callers | |
|---|---|---|
| 4 | 1 | |
| 711 | 71 | |
| 3.1% | - | |
| 8.4 | 2.9 | |
| 4 days ago | 4 months ago | |
| Python | Python | |
| Apache License 2.0 | Apache License 2.0 |
Stars - the number of stars that a project has on GitHub. Growth - month over month growth in stars.
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covalent
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Remote execution of code
Pretty interesting request, if SSH is not used, i would try using something like dask which uses tcp to connect and execute assuming your workers are in another machine.I also think something like covalent can be used to extend your own custom plugin in their ecosystem to connect how you want. We have a very custom private plugin written on top of covalent's to have a custom protocol to connect our central on-prem GPU machines to our local laptops that is rpc based, mostly for high performance as well as some mandate security from where the GPU machines are. Once done it is pretty much something like
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Prefect alternatives meant for Slurm (HPC)
Does anyone here have any suggestions of alternatives tailored for Slurm on HPC? I know Covalent is one option, but I'm curious about others as well. Ideally the platform should be Pythonic, have a GUI, and be reasonably active/well-maintained.
- Show HN: Covalent – distributed computing for ML, HPC and Quantum (open source)
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Your strategies for offloading computation
Came across this new tool exactly for this - https://github.com/AgnostiqHQ/covalent
sv-callers
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Do you know how to get CNVs out of WES data sorted.bam files? (Free)
Generally, you have multiple ways to tackle this kind of a problem. For short read sequencing you have two types of CNV detection - readdepth based and paired-end based. CNVpytor (CNVnator) for example, is the former. You also have manta and lumpy. A lot of good pipelines use more than one SV caller and integrate them. For example: https://github.com/GooglingTheCancerGenome/sv-callers
What are some alternatives?
SmartSim - SmartSim Infrastructure Library.
gatk4-genome-processing-pipeline-azure - Workflows used for processing whole genome sequence data + germline variant calling.
kestra - Infinitely scalable, event-driven, language-agnostic orchestration and scheduling platform to manage millions of workflows declaratively in code.
metaGEM - :gem: An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data
cadence-python - Python framework for Cadence Workflow Service
aviary - A hybrid assembly and MAG recovery pipeline (and more!)
mlnotify - 🔔 No need to keep checking your training - just one import line and you'll know the second it's done.
zarp - The Zavolab Automated RNA-seq Pipeline
dagster - An orchestration platform for the development, production, and observation of data assets.
hecatomb - hecatomb is a virome analysis pipeline for analysis of Illumina sequence data
bytehub - ByteHub: making feature stores simple
galaxy - Data intensive science for everyone.