Table 8 Assembler software for short-read assembly
Assembler | Assembly method | Version | Release date | Parameter |
|---|---|---|---|---|
ABySS [28] | Single k-mer De Bruijn graph | 2.2.3 | 27/09/2019 | -k 96 / -k 128 |
A5-miseq [29] | Automated pipeline including read cleaning, k-mer based error correction, assembly with IDBA and misassembly correction | 20,160,825 | 25/08/2016 | default |
IDBA [30] | Accumulated De Bruijn graph with iteratively increased k-mer size | 1.1.3 | 11/07/2016 | --mink 20 --maxk 124 |
MaSuRCA [31] | DeBruijn graph and Overlap-Layout-Consensus (OLC) | 3.3.4 | 13/09/2019 | GRAPH_KMER_SIZE = auto cwgErrorRate = 0.25 CLOSE_GAPS = 1 |
MIRA [32] | ‘High-quality alignments first’ contig building strategy with iterative removal of technology-specific errors | V5rc2 | 26/02/2019 | Default |
SGA [33] | String graph based on read pair overlaps (using FM index) | 0.10.15 | 05/08/2016 | -m 111 --min-branch-length 400 |
SPAdes [35] | Multi-kmer De Bruijn graph | 3.13.0 | 16/10/2018 | --cov-cutoff auto --careful |
Tadpole [36] | Single k-mer-based assembly with read extension optimized for correctness | BBMap 35.85 | 16/08/2016 | Default |
VelvetOptimiser [88] | Single k-mer De Bruijn graph with optimised N50 | 2.2.6 Velvet: 1.2.10 | 03/08/2017 05/07/2018 | -s 97 -e 127 -x 10 |