Welcome to the Seq2Fun!

Seq2Fun is an ultrafast, all-in-one functional profiling tool for RNA-seq data analysis for organisms without reference genomes.

Key features of Seq2Fun

  • Ultra-fast: Seq2Fun is > 120 times faster (~ 2 million reads / minute) than the conventional RNA-seq workflow.
  • Extremely low memory cost: Seq2Fun consumes as little as 2.27 GB memory and can run on a standard PC with 8 threads and 16 GB memory.
  • Highly efficient: Seq2Fun can finish a typical RNA-seq dataset within several hours on a standard PC in stead of several days or even weeks by conventional RNA-seq workflow on a high-performance server.
  • Reference-free: Seq2Fun does not require the genome or transcriptome reference of the organism; it is also transcriptome de novo assembly-free.
  • Highly accurate: Seq2Fun generates KO abundance with R2 value as high as 0.93 comparing with the ground truth.
  • All-in-one: Seq2Fun directly takes raw RNA-seq reads as input and output gene abundance table without any intermediate file writing and loading, making I/O very efficient.
  • Multifunctional: Seq2Fun generates 6 levels of output files, including KO abundance table, hit pathway table, hit species table, reads KO table, a html report summarizing these tables and reads quality check, as well as output mapped clean reads for further analysis such as gene assembly.
  • Highly flexible: Seq2Fun supports RNA-seq analysis on particular genes or groups of organisms using customized database.
  • Easy to use: Seq2Fun requires minimal programing skills.

Citing Seq2Fun

Peng Liu, Jessica Ewald, Jose Hector Galvez, Jessica Head, Doug Crump, Guillaume Bourque, Niladri Basu, Jianguo Xia. (2021) “Ultrafast functional profiling of RNA-seq data for nonmodel organismsGenome Research (10.1101/gr.269894.120)