id	author	title	date	pages	extension	mime	words	sentences	flesch	summary	cache	txt
cord-016108-jlono0x7	Marthaler, Douglas	Next-Generation Sequencing for Porcine Coronaviruses	2015-09-10		.txt	text/plain	1439	97	57	In this chapter, we describe a method to deep genome sequence porcine coronavirus on the Illumina MiSeq, avoiding the number of contaminating reads associated with the host and other microorganisms. (e) Remap the reads to the contig to verify accurate generation of the viral genome and suffi cient coverage. (a) Open the SeqManNGen program, select reference-based assembly, and load the Susscrofa genome and the correlating paired fastq fi les to the sample. However, the concentration by RT-PCR may not indicate successful generation of the complete viral genome since total RNA was used in the library preparation. If libraries have limited host contamination and have an acceptable concentration of viral RNA (Ct value <25), a 1 million read output per sample should be suffi cient for assembly. Since the MiSeq generates reads from total RNA, host reads need to be removed to facilitate de novo assembly, which can be done by fi rst mapping the reads to the swine genome and saving the unmapped reads.	./cache/cord-016108-jlono0x7.txt	./txt/cord-016108-jlono0x7.txt