QUAST: quality assessment tool for genome assemblies

By Alexey A. Gurevich, Vladislav Saveliev, Nikolay Vyahhi, Glenn Tesler. Bioinform., 2013

4,723 citations recorded by the source corpus.

Subfields: Genetics, Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/9cf2292f27609a92ad78fd50985db366de688777

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Citations in the corpus

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes (2015, background): “The quality of isolate genomes has traditionally been evaluated using assembly statistics such as N50 (Salzberg et al. 2012; Gurevich et al. 2013), whereas single-cell and metagenomic studies have relied on the presence and absence of universal single-copy “ marker ” genes for estimating genome…”
Circlator: automated circularization of genome assemblies using long sequencing reads (2015, methodology): “All assemblies, both pre-and post-Quiver, were evaluated using QUAST [25] version 2.3 with the options --gage -”
hybridSPAdes: an algorithm for hybrid assembly of short and long reads (2016, methodology): “While QUAST reports many assembly metrics, the benchmarking tables below are limited to NG50, NG75, LG50, the length of the longest contig, and the number of misassemblies (MA), where NG50 is the length for which the collection of all contigs of that length or longer covers at least half of the refe”
ABySS 2.0: resource-efficient assembly of large genomes using a Bloom filter (2016, positive): “Often assembly algorithms are also validated using data from resequencing experiments, where assembled sequences are compared against a reference genome for their correctness in addition to their contiguity (Gurevich et al. 2013).”
A5-miseq: an updated pipeline to assemble microbial genomes from Illumina MiSeq data (2014, methodology): “Source code and precompiled binaries for Mac OS X 10.6+ and Linux 2.6.15+ are available from http://code.google.com/p/ngopt 4 Contact: aaron.darling@uts.edu.au”
MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph (2014, methodology): “QUAST (Gurevich, et al., 2013) was used to evaluate the assembled contigs (Table 1).”
SSPACE-LongRead: scaffolding bacterial draft genomes using long read sequence information (2014, methodology): “It is therefore adviced to assess the quality of an assembly using a dedicated tool, such as QUAST [21], which gives a complete overview of different quality metrics.”
Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads (2016, neutral): “3)[28].”
TGS-GapCloser: A fast and accurate gap closer for large genomes with low coverage of error-prone long reads (2020, neutral): “2 describes the improvements in the assembly evaluation given by QUAST (QUAST, RRID:SCR 001228) [41] after gap closure.”
A complete bacterial genome assembled de novo using only nanopore sequencing data (2015, methodology): “The initial draft assembly has 3,949 mismatches (85 per 100kb) and 47,395 indels of ≥ 1 base (1,021 errors per 100kb), as determined by the QUAST validation tool when compared to the E. coli K-12 MG1655 reference genome (NC 000913.3) 14 .”