Welcome to Salmon’s documentation!# Contents: Requirements Binary Releases Requirements for Building from Source Installation Salmon Using Salmon Preparing transcriptome indices (mapping-based mode) Quantifying in mapping-based mode Quantifying in alignment-based mode Description of some important options What’s this LIBTYPE? Output Misc References Alevin Using Alevin Providing multiple read files to Alevin Description of important options Single-cell protocol specific notes Output Output Quality Check Tutorial & Parsers Alevin Logs Misc BibTex DOI References Salmon Output File Formats Quantification File Command Information File Auxiliary Files Fragment Library Types Indices and tables# Index Module Index Search Page