Table 7.

Recommendations for de novo tool selection under varying conditions

Read property			Small genome			Large genome
	GC	Read	High N50	High SC	Low AER	High N50	High SC	Low AER
SE	Low	Short	Eu, SS	SS	Ed, AB, Ve	Eu, SO, Ed	SO, Ed, AB, Ve	Ed, AB, Ve
		Long	SS, SO	SS	AB, Ve	SO	SO, Ed, AB, Ve	AB, Ve
	High	Short	Eu, SO	SS, SO	AB, Ve, Ed	SO, Eu	SO	AB, Ve, Ed
		Long	SO, Ed, AB, Ve	SS, SO	AB, Ve	SO, Ed	SO	AB, Ve
PE	Low	Short	SO, SS, AB, Ve	AB, SS, Ve, SO	AB, Ve, SO	SO, AB, Ve	AB, SO, Ve	AB, Ve, SO
		Long	SO, SS	AB, SS, SO, Ve	AB, Ve, SO	SO, AB, Ve	AB, SO, Ve	AB, Ve, SO
	High	Short	SO	AB	AB, Ve, SO	SO	AB	AB, Ve, SO
		Long	SO, AB, Ve	AB	AB, Ve, SO	SO, AB, Ve	AB	AB, Ve, SO

Requirements of assembly performance includes high N50, high sequence coverage (SC), low assembly error rate (AER). For different requirements, we recommend some de novo tools with order of priority according to properties of sequence reads, including single-end/paired-end, GC content, read length and sequence length. SE, single end reads; PE, paired end reads; Eu, Euler-sr; SS, SSAKE; Ed, Edena; AB, ABySS; Ve, Velvet; SO, SOAPdenovo.