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omicverse-single-cell-kb-alignment

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Triggerable kb reference and count for scRNA-seq.

Data & Analytics#workflow#reference#alignment#single-cell#omics#counting
AuthorStarlitnightly
Version1.0.0
Installs0

System Documentation

What problem does it solve?

This Skill provides a repeatable way to build a kb reference from FASTA/GTF inputs and quantify single-cell FASTQs into count matrices using OmicVerse alignment wrappers, stopping at the count stage to keep downstream QC/preprocessing separate.

Core Features & Use Cases

  • Build a kb reference: generate index and t2g mappings from fasta/gtf data.
  • Count cells: quantify reads into count matrices with ov.alignment.single.count, producing outputs ready for downstream analysis.
  • Flexible workflows: supports standard and nucleus modes and aligns with downstream preprocessing pipelines for single-cell RNA-seq.

Quick Start

Install the skill, then build the reference with ov.alignment.single.ref(...) and run ov.alignment.single.count(...) on your FASTQs.

Dependency Matrix

Required Modules

None required

Components

referencesassets

💻 Claude Code Installation

Recommended: Let Claude install automatically. Simply copy and paste the text below to Claude Code.

Please help me install this Skill:
Name: omicverse-single-cell-kb-alignment
Download link: https://github.com/Starlitnightly/omicverse-skills/archive/main.zip#omicverse-single-cell-kb-alignment

Please download this .zip file, extract it, and install it in the .claude/skills/ directory.
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