id	author	title	date	pages	extension	mime	words	sentences	flesch	summary	cache	txt
cord-302085-xyru2q9o	Shepard, Samuel S.	Viral deep sequencing needs an adaptive approach: IRMA, the iterative refinement meta-assembler	2016-09-05		.txt	text/plain	10341	540	50	IRMA provides segment level read sorting based on LABEL, a sequence classification tool ideal for segmented genomes [11] ; iteratively gathers reads and iteratively edits the reference templates to account for high population diversity and mutational rates; and provides redesigned variant calling (heuristics as well as statistical tests) and phasing to allow for the analysis of diverse viral sub-populations. We solve these referenced-based assembly complications by using iterative refinement-moving the reference template closer to the reads-to obtain quality assemblies with increased sensitivity to distant and novel reads BLAT* or LABEL match sort into segments rough align chimeric low quality high quality templates removed module consensuses [1] de-multiplexed sample [1] [2] [3] [4] [5] READ GATHERING: do steps [3] to [5] optimize assembly [6] insertion, deletion, substitution merge reads+ [7] call variants [8] phase variants [9] Perl scripts, samtools, R Steps in (b) are also labeled under the steps of (a) where they correspond genetic variants.	./cache/cord-302085-xyru2q9o.txt	./txt/cord-302085-xyru2q9o.txt