ContigExtender: a new approach to improving de novo sequence assembly for viral metagenomics data

BMC Bioinformatics

Table 1 Metagenome datasets used to evaluate ContigExtender performance

Data set	Sample	Read length	#reads	Genome type	Sequencing platform	Description
NIBSC	NIBSC-26	250	8.55 M	25 different human RNA and DNA viral pathogens	MiSeq	Multiplexed viral standards
Animal	Mosquito Pool20	150	0.81 M	Culex Iflavi-like virus Mesoniviridae	HiSeq4000	Mosquito pool
Animal	Mosquito Pool27	150	1.54 M	Culex Iflavi-like virus Mesoniviridae	HiSeq4000	Mosquito pool
Animal	Fish1-pool	250	2.30 M	Enterococcus virus	MiSeq	Fish tumor mass
Animal	Dog-pool	250	1.31 M	Uncultured crAssphage	MiSeq	Dog stool sample
Human	12-110034-veqrpcr	250	0.53 M	Hepacivirus C	Miseq	Human blood sample
Human	47210-feces	250	1.90 M	Escherichia virus	Miseq	Human stool sample
Human	Amazon-4B	250	0.81 M	Norwalk Virus	Miseq	Human stool sample
Human	Amazon-3D	250	0.38 M	Husavirus	Miseq	Human stool sample
Human	Amazon-17D	250	1.61 M	Husavirus	Miseq	Human stool sample
Human	Amazon-6D	250	0.47 M	Human Cosavirus	Miseq	Human stool sample
Human	Amazon-S10-CNI-055	250	0.95 M	Betapapillomavirus	Miseq	Human nasal swab sample

Genomic sequences from NIBSC, Animal and Human metagenome datasets represent various pathogen types, genome sizes, sample backgrounds, and sequencing outputs that were encountered in real world metagenome and clinical applications using NGS

ISSN: 1471-2105