BIGrat: a repeat resolver for pyrosequencing-based re-sequencing with Newbler

BMC Research Notes

Table 1 The performance of Newbler and Newbler-BIGrat in assembling different genomes

Reference ¹	Assembly method	Genome size (bp)	Contig length (bp)	Contig number	Contig NG50 ²	Contig LG50 ³	Gap-filling number ⁴	Gap-filling length ⁴
Rice PA64S nuclear	BWA-SW	372,317,567	328,243,169	55,092	17,903	4,534	\	\
	Newbler		353,856,308	61,922	19,383	5,351	\	\
	Newbler-BIGrat		362,123,475	41,838	28,677	3,671	20,084	8,267,167
Acinetobacter baumannnii	BWA-SW	3,991,133	3,681,865	133	101,163	14	\	\
	Newbler		3,684,532	119	128,034	12	\	\
	Newbler-BIGrat		3,717,247	104	173,210	9	15	32,715
Rice PA64S mt	BWA-SW	490,673	405,286	5	234,879	1	\	\
	Newbler		273,171	104	1,022	13	\	\
	Newbler-BIGrat		464,774	1	464,774	1	103	191,603
Rice PA64S cp	BWA-SW	134,551	133,024	3	58,368	2	\	\
	Newbler		113,344	56	81,038	1	\	\
	Newbler-BIGrat		134,156	1	134,156	1	55	20,812

Note:
1. The rice reference is a set of pseudomolecules from Rice Genome Annotation Project (version 6.1) (http://rice.plantbiology.msu.edu) for nuclear, mt and cp genomes. The Acinetobacter baumannii reference genome is the complete sequence from isolate ACICU (accession number: NC_010611). 2. NG50 is the contig length at which 50% of the total genome length is covered. 3. LG50 is the contig number at which 50% of the total genome length is covered. 4. Comparison between Newbler and Newbler-BIGrat.

ISSN: 1756-0500