TY - JOUR

T1 - Versatile genome assembly evaluation with QUAST-LG

AU - Mikheenko, Alla

AU - Prjibelski, Andrey

AU - Saveliev, Vladislav

AU - Antipov, Dmitry

AU - Gurevich, Alexey

N1 - Conference code: 2018

PY - 2018/7/1

Y1 - 2018/7/1

N2 - Motivation: The emergence of high-throughput sequencing technologies revolutionized genomics in early 2000s. The next revolution came with the era of long-read sequencing. These technological advances along with novel computational approaches became the next step towards the automatic pipelines capable to assemble nearly complete mammalian-size genomes. Results: In this manuscript, we demonstrate performance of the state-of-the-art genome assembly software on six eukaryotic datasets sequenced using different technologies. To evaluate the results, we developed QUAST-LG?a tool that compares large genomic de novo assemblies against reference sequences and computes relevant quality metrics. Since genomes generally cannot be reconstructed completely due to complex repeat patterns and low coverage regions, we introduce a concept of upper bound assembly for a given genome and set of reads, and compute theoretical limits on assembly correctness and completeness. Using QUAST-LG, we show how close the assemblies are to the theoretical optimum, and how far this optimum is from the finished reference.

AB - Motivation: The emergence of high-throughput sequencing technologies revolutionized genomics in early 2000s. The next revolution came with the era of long-read sequencing. These technological advances along with novel computational approaches became the next step towards the automatic pipelines capable to assemble nearly complete mammalian-size genomes. Results: In this manuscript, we demonstrate performance of the state-of-the-art genome assembly software on six eukaryotic datasets sequenced using different technologies. To evaluate the results, we developed QUAST-LG?a tool that compares large genomic de novo assemblies against reference sequences and computes relevant quality metrics. Since genomes generally cannot be reconstructed completely due to complex repeat patterns and low coverage regions, we introduce a concept of upper bound assembly for a given genome and set of reads, and compute theoretical limits on assembly correctness and completeness. Using QUAST-LG, we show how close the assemblies are to the theoretical optimum, and how far this optimum is from the finished reference.

KW - DE-NOVO

KW - METAGENOME ASSEMBLIES

KW - SHORT READS

KW - ALGORITHMS

KW - BENCHMARK

KW - SOFTWARE

KW - GAUGE

KW - SCALE

KW - TOOL

UR - http://www.scopus.com/inward/record.url?scp=85050791638&partnerID=8YFLogxK

UR - http://www.mendeley.com/research/versatile-genome-assembly-evaluation-quastlg

U2 - 10.1093/bioinformatics/bty266

DO - 10.1093/bioinformatics/bty266

M3 - Article

AN - SCOPUS:85050791638

VL - 34

SP - i142-i150

JO - Bioinformatics

JF - Bioinformatics

SN - 1367-4803

IS - 13

T2 - Intelligent Systems for Molecular Biology

Y2 - 6 July 2018 through 10 July 2018

ER -