Clinical metagenomic identification of Balamuthia mandrillaris encephalitis and assembly of the draft genome: the continuing case for reference genome sequencing

Table 2 Sequencing runs and genome assembly details

Sequencing run	Raw reads	Filtered reads	Read length	Library prep
MP1^a	3845734	N/A	2 × 80 bp	Nextera Mate-Pair
MP2^a	31223454	12095792	2 × 80 bp	Nextera Mate-Pair
MP3^a	14121900	4397510	2 × 250 bp	Nextera Mate-Pair
PE1^b	213604902	29314946	2 × 250 bp	Nextera XT
Genome Assembly^c	Contigs	N50 (bp)	Assembly Size
Mitochondria	1	41,656	41,656
Contigs	31,194	3,411	48,938,887
Scaffolds	26,811	19,415	49,120,517
Gap-fill	26,811	19,012	48,939,625
Final assembly (minus <500 bp, contaminants)	14,699	26,144	44,270,879

^aThree runs of a Nextera mate-pair library of Balamuthia strain 2046 from axenic culture sequenced on an Illumina MiSeq
^bNextera XT paired-end library of strain 2046 sequenced on an Illumina HiSeq
^cAssembly of mitochondrial genome from MP1 library, of whole-genome from all four libraries