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omicverse-single-cell-kb-alignment

Build kallisto|bustools references and quantify single-cell FASTQ libraries into count matrices.

13|2|Updated Apr 5, 2026
Search Tags:#alignment#single-cell#omicverse#fastq#kallisto#count matrix#bustools
One-click install
npx skills add https://github.com/omicverse/omicverse-skills --skill omicverse-single-cell-kb-alignment-omicverse
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: omicverse-single-cell-kb-alignment
Source: https://github.com/omicverse/omicverse-skills/tree/main/src/omicverse_skills/skills/single-cell-kb-alignment
Command: npx skills add https://github.com/omicverse/omicverse-skills --skill omicverse-single-cell-kb-alignment-omicverse

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) and assets (resource) components.

What problem does it solve?

This Skill turns OmicVerse single-cell kb alignment notebooks into a reusable workflow for building references and generating count matrices from FASTQ files. It removes the guesswork around choosing reference settings, matching sequencing chemistry, and checking whether the outputs were created correctly.

Core Features & Use Cases

  • Build a kallisto|bustools reference from FASTA and GTF inputs or reuse an existing bundle.
  • Quantify single-cell libraries with technology-aware options such as standard, nucleus, and barcode filtering paths.
  • Validate emitted outputs like matrix files and AnnData handoff artifacts before passing the data to downstream preprocessing.
  • Use case: a researcher receives paired-end 10x reads and wants a clean count matrix ready for single-cell QC and clustering.

Quick Start

Ask the AI to build a kb reference from your FASTA and GTF files, quantify the matching single-cell FASTQs, and return the count matrix paths for downstream analysis.

Frequently Asked Questions about omicverse-single-cell-kb-alignment

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I build a kallisto bustools reference for single-cell RNA-seq alignment?▼

To build a kb reference for single-cell RNA-seq alignment, provide matching FASTA and GTF input files to generate a reference index bundle for quantifying FASTQ libraries.

Can I quantify single-cell FASTQ files into a count matrix using kallisto bustools?▼

Yes, you can quantify single-cell FASTQ libraries into count matrices using kallisto bustools by selecting the correct sequencing chemistry and applying technology-aware counting options.

What FASTA and GTF inputs do I need to create a kb reference index?▼

Creating a kb reference index requires matching FASTA and GTF input files to generate the transcriptome reference, or you can reuse a prebuilt index bundle for quantification.

Does kallisto bustools alignment support generating AnnData objects directly from FASTQ?▼

Yes, kallisto bustools alignment supports optional AnnData output generation directly from FASTQ files, producing h5ad artifacts ready for downstream single-cell QC and clustering.

What's the best way to handle nucleus and barcode filtering during single-cell counting?▼

The best way to handle nucleus and barcode filtering during single-cell counting is using technology-aware options in kallisto bustools that apply specific filtering paths based on chemistry selection.

Why does my single-cell count matrix need validation before downstream preprocessing?▼

Your single-cell count matrix needs validation before downstream preprocessing to verify that emitted matrix files and AnnData handoff artifacts were created correctly and match expected outputs.

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