id	author	title	date	pages	extension	mime	words	sentences	flesch	summary	cache	txt
cord-267500-x3u9i1vq	Rose, Rebecca	Challenges in the analysis of viral metagenomes	2016-08-03		.txt	text/plain	5928	308	40	Notable technical challenges have impeded progress; for example, fragments of viral genomes are typically orders of magnitude less abundant than those of host, bacteria, and/or other organisms in clinical and environmental metagenomes; observed viral genomes often deviate considerably from reference genomes demanding use of exhaustive alignment approaches; high intrapopulation viral diversity can lead to ambiguous sequence reconstruction; and finally, the relatively few documented viral reference genomes compared to the estimated number of distinct viral taxa renders classification problematic. The Illumina short read platform is widely used for analyses of viral genomes and metagenomes, and, given sufficient sequencing coverage, enables sensitive characterization of lowfrequency variation within viral populations (e.g. HIV resistance mutations as low as 0.1% (Li et al. We recently proposed a method based on numerical sequence representations and digital signal processing data transformation (SPDT) approaches to reduce the size of working datasets, permitting fast and sensitive read alignment and de novo assembly of diverse viral populations (Tapinos et al.	./cache/cord-267500-x3u9i1vq.txt	./txt/cord-267500-x3u9i1vq.txt