Welcome to the documentation for alevin-fry

What is alevin-fry?

Alevin-fry is a program exposing a suite of tools for single-cell sequencing analysis. It makes use of the selective-alignment and tag processing framework of alevin.

Contents:

• Overview
• Other resources for alevin-fry
  • Tutorials
  • FAQ
  • Quality Control
  • Easy loading of USA-mode data
• Installing alevin-fry
  • Installing with bioconda
  • Installing from source
• Getting Started
  • Running the alevin-fry pipeline
  • Detailed information on the alevin-fry commands
• alevin-fry commands
  • generate-permit-list
  • collate
  • quant
  • infer
• License

Indices and tables

• Index

• Module Index

• Search Page