| Functions | Applications | Input files | Main output files | Programs | References |
| Assemble Unmapped Reads | De novo assemble unmapped reads, remove redundancy of transcript fragments and re-assemble transcript fragments | Unmapped reads | Assembled transcript sequences (Fasta) | Trinity (version 2.2.0; https://github.com/trinityrnaseq/trinityrnaseq/wiki) | Grabherr et al., 2011 |
| CD-HIT-EST (version 4.6.8; http://weizhongli-lab.org/cd-hit/) | Li et al., 2006 | ||||
| CAP3 (version 12/21/07; http://seq.cs.iastate.edu/cap3.html) | Huang et al., 1999 |