Open source alternatives to pacsomatic
24 open source AI Skills apps to use instead, best rated first.
Top picks
- G
github-ops
Launchgithub-ops is an agent skill from the ECC collection by affaan-m, listed on skills.sh. It manages a GitHub repository with a focus on community health, CI reliability and the experience of contributors. It covers triaging issues by classify
Open source
- O
opensource-pipeline
Launchopensource-pipeline is an agent skill from the ECC collection by affaan-m, listed on skills.sh. It prepares a private project for safe public release through a three-stage pipeline. The fork stage strips secrets from a copy. The sanitise st
Open source
- A
andrej-karpathy-skills
Launchandrej-karpathy-skills is a single CLAUDE.md file from the multica-ai project that is meant to improve how Claude Code behaves on coding tasks. It is derived from Andrej Karpathy's public observations about LLM coding pitfalls. The file dis
Open source
- M
microsoft/markitdown
Launchmarkitdown-mcp is the MCP server package for MarkItDown, Microsoft's tool for converting many file formats to Markdown for language models. It is a lightweight server that runs over stdio, Streamable HTTP or SSE, and exposes one tool, conve
Open source
- O
od-contribute
Launchod-contribute is an agent skill in the OpenDesign project that provides a guided, one-click contribution flow to the OpenDesign repository, written so that people without a coding background can send a real pull request. It is locked to the
Open source
- G
github-deep-research
Launchgithub-deep-research is an agent skill from the DeerFlow project that researches a single GitHub repository in several rounds and writes a report in Markdown. It is for requests that need more than a README summary, such as a comprehensive
Open source
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Learn Claude Code
by shareAI-lab - A really interesting analysis of how coding agents like Claude
About pacsomatic
pacsomatic
Prepares and launches nf-core/pacsomatic matched tumor-normal PacBio HiFi
pacsomatic is an agent skill for preparing and launching the nf-core pacsomatic workflow, which analyses matched tumour and normal PacBio HiFi genomics data from unaligned BAM files. The skill includes a helper script that prepares one matched tumour and normal pair, generates a samplesheet and reproducible launch files, and then runs the Nextflow driver locally or submits it to a scheduler. The pipeline realigns the input BAM files, and the helper is for unaligned HiFi BAMs and optional PacBio index files. The skill warns against substituting short-read data, and against treating a BAM file name as evidence of the platform, the matched identity or methylation information. The reviewed upstream development commit is pinned by default. GitHub had no releases or tags on 1 October 2026, even though an internal manifest names version 1.0.0, so the helper pins the commit and does not invent a release tag. The skill describes its workflow as a development workflow that has been reviewed against source, not a clinically validated assay. Its guide records the sources and the scientific checks. Use it for research on matched cancer genomes sequenced with PacBio HiFi.
- Price
- Free
- Made by
- k-dense-ai
- Category
- AI Skills
- Website
- github.com/k-dense-ai/scientific-agent-skills/pacsomatic