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Table 8 Assembler software for short-read assembly

From: Testing assembly strategies of Francisella tularensis genomes to infer an evolutionary conservation analysis of genomic structures

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