Table 2. Next-generation genome assemblers: Architecture.

Assemblers	Preprocessing Filtering	Graph Construction Process	Graph Simplification Process	Postprocessing Filtering	Ref.
Newbler GS de novo assembler	N/A	Overlap-based	-Merging consecutive nodes	-Building contigs	[19]
Edena	N/A	Overlap-based	-Removing dead ends-Removing transitive edges-Dealing with bubbles	-Building contigs	[14]
Celera CABOG wgs-assembler	-Remove and correct erroneous reads	Overlap-based	-Merging consecutive nodes-Removing dead ends	-Building contigs-Detecting misassembled contigs-Merging contigs and fill gaps-Removing transitive edges-Detecting repeated contigs-Building scaffolds	[21], [23]
Shorty	N/A	Overlap-based	N/A	-Building contigs-Detecting misassembled contigs-Merging contigs and fill gaps-Building scaffolds	[15]
Forge	-Remove erroneous reads	Overlap-based	N/A	-Building contigs-Building scaffolds	[11]
SGA	-Remove and correct erroneous reads	Overlap-based	-Removing dead ends-Dealing with bubbles	-Building contigs-Building scaffolds	[30]
Readjoiner	-Remove and correct erroneous reads	Overlap-based	-Removing dead ends-Dealing with bubbles	-Building contigs	[13]
Fermi	-Correct erroneous reads	Overlap-based	-Dealing with bubbles	-Building contigs	[60]
Euler-SR	-Remove and correct erroneous reads	K-mer–based	-Merging consecutive nodes-Removing dead ends-Dealing with bubbles-Removing tangles	-Building contigs-Building scaffolds	[10]
ALLPATHS-LG	-Remove and correct erroneous reads	K-mer–based	-Removing dead ends-Dealing with bubbles	-Building contigs-Building scaffolds	[7], [18], [59]
Velvet	-Remove erroneous reads	K-mer–based	-Merging consecutive nodes-Removing dead ends-Dealing with bubbles	-Building contigs-Merging contigs and fill gaps-Detecting and resolving repeated contigs-Building scaffolds	[35]
ABySS	N/A	K-mer–based	-Removing dead ends-Dealing with bubbles	-Building contigs-Merging contigs	[31]
SOAPdenovo	-Correct erroneous reads	K-mer–based	-Merging consecutive nodes-Removing dead ends-Dealing with bubbles-Removing tangles	-Building contigs-Merging contigs and fill gaps-Removing transitive edges-Detecting repeated contigs-Building scaffolds	[17]
SparseAssembler	N/A	Sparse k-mer–based	-Removing dead ends-Dealing with bubbles	-Building contigs	[34]
SSAKE	N/A	Greedy-based	N/A	-Building contigs	[33]
SHARCGS	-Remove erroneous reads	Greedy-based	N/A	-Building contigs	[12]
Vcake	N/A	Greedy-based	N/A	-Building contigs	[74]
QSRA	N/A	Greedy-based	N/A	-Building contigs	[75]
Taipan	N/A	Hybrid-based	-Removing transitive edges	-Building contigs	[29]