Whole genome capture of vector-borne pathogens from mixed DNA samples: a case study of Borrelia burgdorferi

BMC Genomics

Table 2 Pairwise comparison of multiplex captures. Comparison of B. burgdorferi capture efficiency from tick genomic libraries that were captured twice in different reaction capture using different multiplexing scheme

Sample	No. pooled samples ^a	Total reads (bp)	B. burgdorferi mapped reads (bp) ^b	B. burgdorferi efficiency ^c	Tick mapped reads (bp) ^d	Tick efficiency
Bbcap4	1	27,557,241	2,644,289	0.10	6,032,190	0.15
Bbcap4	4	2,514,653	1,399,218	0.56	503,015	0.14
Bbcap2	4	3,169,012	1,939,221	0.61	616,781	0.12
Bbcap2	10	1,445,990	927,938	0.64	281,094	0.15
Bbcap30	4	11,002,588	8,744,400	0.79	582,618	0.03
Bbcap30	10	4,574,392	3,780,942	0.83	244,753	0.04
Bbcap31	10	3,903,612	3,328,957	0.85	269,657	0.05
Bbcap31	20	3,097,722	2,638,052	0.85	199,022	0.05
Bbcap6	10	4,466,415	3,605,584	0.81	260,144	0.04
Bbcap6	20	2,694,537	2,190,349	0.81	136,170	0.04

^aNumber of sample mutliplexed in a single capture reaction
^bTotal number of sequenced bases mapped to the B. burgdorferi B31 reference genome after removal of PCR and optical duplicates
^cProportion of sequences that mapped to the reference genome after removal of PCR and optical duplicates
^dTotal number of sequenced bases mapped to the I .scapularis draft assembly [16, 17] after removal of PCR and optical duplicates

ISSN: 1471-2164