A review of software for analyzing molecular sequences

BMC Research Notes

Table 2 Defaults for each of the reviewed pipelines

	Mothur	QIIME	WATERS	RDPipeline	VAMPS	Genboree	SnoWMAn
Minimum reads	0 – User defined	200 bp	500 bp	150 bp	200 bp	0 – User defined	150 bp
Maximum reads	Not bounded – User defined	1000 bp		500 bp	1000 bp	Not bounded – User defined
Max homopolymers	Not bounded – User defined	6 bp
Number of allowable ambiguous bases (AB) or N’s	Not bounded - User defined (recommended AB = 0)	AB = 6		N = 0	N = 0	Not bounded – User defined	N = 0
Minimum quality score	0 – User defined	25		20		0 – User defined	20
Alignment method	Needleman	Pynast	Infernal	Infernal	GAST	Pynast	Varies by pipeline method
Chimera	User defined	User defined	Mallard	Uchime		ChimeraSlayer

ISSN: 1756-0500