QUAST: quality assessment tool for genome assembles

By Vladislav Saveliev, Alexey A. Gurevich. 2013

540 citations recorded by the source corpus.

Subfields: Genetics, Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/3c299b3a60c7f0b525d3eb5d37de13bf94eb1394

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Citations in the corpus

Versatile genome assembly evaluation with QUAST-LG (2018, background): “Gurevich et al. (2013) define a misassembly breakpoint as a position in an assembled contig where the flanking sequences align to opposite strands (inversion), or to different chromosomes (translocation), or the inconsistency size d (a gap or an overlap) between the alignments of the left and right ”
Completing bacterial genome assemblies with multiplex MinION sequencing (2017, background): “Short reads cannot resolve all genomic repeats, and fragmented assemblies comprising hundreds of discrete contigs are often the best possible outcome [4].”
Rcorrector: efficient and accurate error correction for Illumina RNA-seq reads (2015, methodology): “We evaluated the alignment outcome as described earlier and separately used the package QUAST [25] to assess the quality of the resulting genome assemblies.”
Contiguous and accurate de novo assembly of metazoan genomes with modest long read coverage (2015, unknown): “Assessment of assembly quality We assessed assembly quality using the Quast software package (22) and the quality assessment scripts used in the GAGE study (23).”
SKESA: strategic k-mer extension for scrupulous assemblies (2018, methodology): “Count SKESA SPAdes MegaHit IDBA ABySS 0 214 172 128 224 250 1 83 98 91 76 79 2 40 43 66 32 26 3 13 30 30 8 6 4 9 12 18 11 9 5 7 7 15 5 8 6 2 3 10 7 0 7 2 0 5 1 1 8 1 1 3 2 0 9 0 0 2 2 0 10+ 10 15 13 13 2 Median 0 1 1 0 0 1 Table S3: Mismatches per 100 Kb as reported by QUAST for benchmark and contam”
Assembling Single-Cell Genomes and Mini-Metagenomes From Chimeric MDA Products (2013, unknown): “We use metrics NA50 and NGA50, introduced and justiﬁed in Gurevich et al. (2013), instead of the standard N50 or NG50 metrics, to overcome these problems.”
plasmidSPAdes: Assembling Plasmids from Whole Genome Sequencing Data (2016, methodology): “Table 2 lists the following statistics that were generated using QUAST software (Gurevich et al., 2013) as well as the assembly evaluation software developed specifically for PLASMIDSPADES.”