Converting RNAseq reads from ANY species to functionally annotated count tables

Input: Raw RNAseq files (.fastq.gz)

Web-based processing (this site)
  • Less than 30 GB
  • Register an account (free) and upload your data
Local processing

Species with good reference transcriptomes

Ultra-fast pseudo-alignment based on Salmon or Kallisto algorithm

Species without good reference transcriptomes

Ultra-fast translated alignment using Seq2Fun algorithm
  • Comprehensive support across broad taxonomy levels (~ 12 organism groups)
  • Gene-level annotation based on ortholog searching


  • Gene/transcript quantification table;
  • Gene/transcript annotation table;
    • Best hits
    • KEGG orthologs (KOs)
    • Gene ontologies (GOs)
  • Visualization of functional profiles
Upload the result tables to NetworkAnalyst for in-depth statistical and functional analysis