Table 3 Summary of technical characteristics of the error-correction methods assessed in this study
From: Benchmarking of computational error-correction methods for next-generation sequencing data
Software tool | Data structure | Types of reads accepted | Organism | Journal | In the publication compared to | Tools webpage |
|---|---|---|---|---|---|---|
Bless | Bloom filter and hash table | SE/PE | Human, E. coli, S. aureus | Bioinformatics | SGA, QuorUM, Lighter, BFC, DecGPU, ECHO, HiTEC, Musket, Quake, Reptile | |
Fiona | Partial suffix array | SE | Human, Drosophila, E. coli, C. elegans | Bioinformatics | Allpaths-LG, Coral, H-Shrec, ECHO, HiTEC, Quake | |
Pollux | Hash table | SE/PE | Human, E. coli, S. aureus, mixed genome data | BMC Bioinformatics | Quake, SGA, Bless, Musket, Racer | |
BFC | Bloom filter and hash table | SE/PE | Human, C. elegans | Bioinformatics | Bless, Bloocoo, fermi2, Lighter, Musket, and SGA | |
Lighter | Bloom filter | SE/PE | Human, E. coli, C. elegans | Genome Biology | Quake, Musket, Bless, Soapec | |
Musket | Bloom filter and hash table | SE/PE | Human, E. coli, C. elegans | Bioinformatics | SGA, Quake | |
Racer | Hash table | SE/PE | Human, E. coli, C. elegans, Drosophila, other bacteria | Bioinformatics | Coral, HITEC, Quake, Reptile, SHREC | |
Coral | Hash table | SE/PE | Human, E. coli, S. aureus | Bioinformatics | COMPASS 3.0, HHalign 1.5.1.1 and PSI-BLAST | |
RECKONER | Hash table | SE | Human, S. cerevisiae, C. elegans, M. acuminata | Bioinformatics | Ace, BFC, Bless, Blue, Karect, Lighter, Musket, Pollux, Racer, Trowel | |
SGA | FM-index | SE/PE | Human, C. elegans, E. coli | Genome Research | Velvet, ABySS, SOAPdenovo, Quake, HiTEC |