DMCA
Shotgun Assembler Profiling and Benchmark Development
BibTeX
@MISC{Biswas_shotgunassembler,
author = {Abhishek Biswas and David Gauthier and Desh Ranjan and Mohammad Zubair},
title = {Shotgun Assembler Profiling and Benchmark Development},
year = {}
}
Share
 |
 |
 |
 |
||
OpenURL
Abstract
Abstract — The output quality of assemblers has been under scrutiny [1] due to presence of misassembles in many draft genomes. The assembly quality parameters cited are often not true indicators of a correct assembly and are sensitive to input parameters and genome structure. This paper presents a empirical analysis of assembly quality produced by whole genome assemblers while assembling shotgun sequence data and studies the correlation between assembly quality statistics and sequence similarity score of the original and assembled sequence under varying input parameters such as read length, coverage, repeat length, repeat frequency etc. We experiment with 4 assemblers MIRA [2], Celera WGS [3], Velvet [4] and EulerSR [5]. The first 2 prescribe to the overlap layout consensus (OLC) model [6] and the latter to the de-Brujin Graph model[7]. In this work we use synthetic and actual shotgun reads for experimentation and a benchmark suite for maintaining assembler profiles and capability testing is proposed. The benchmark contains sets of shotgun reads generated from selected bacterial genome segments, plasmids and synthetic sequences which showcase sequence peculiarities shown to cause misassembles during experimentation. The shotgun data simulation process and generation of synthetic paired end libraries is also discussed. Keywords-Genome Assembly, Assembly Quality, I.
Keyphrases
benchmark development shotgun assembler profiling assembly quality assembled sequence assembler profile repeat length shotgun read genome structure assembly quality parameter de-brujin graph model whole genome assembler output quality sequence peculiarity empirical analysis actual shotgun read benchmark suite repeat frequency shotgun sequence data read length true indicator celera wgs overlap layout consensus bacterial genome segment synthetic sequence correct assembly capability testing shotgun data simulation process assembler mira synthetic paired end library many draft genome sequence similarity score quality statistic keywords-genome assembly input parameter
