QUAST-LG

QUAST-LG is an extension of QUAST intended for evaluating large-scale genome assemblies (up to mammalian-size).

QUAST-LG will be included in the upcoming QUAST 5.0 release. Currently you can try the release candidate in the master branch of our GitHub repo.

Short list of the new features:

  • Significant speed up achieved by both use of new fast aligner (minimap2) and the refactoring of alignment analysing modules
  • New k-mer based completeness and correctness metrics
  • BUSCO added for enhanced reference-free analysis
  • Concept of the theoretically optimal assembly

We benchmarked QUAST-LG on five eukaryotic datasets assembled by the leading genome assembly software:

  1. Yeast (S. cerevisiae, genome size: 12.1 Mb): reads (Illumina pair-ends and PacBio); assemblies (4 + optimal, 19 Mb); report
  2. Worm (C. elegans,genome size: 100.3 Mb): reads (Illumina pair-ends and PacBio); assemblies (4 + optimal, 156 Mb); report
  3. Fruit fly (D. melanogaster, genome size: 137.6 Mb): reads (Illumina pair-ends and mate-pairs); assemblies (7 + optimal, 319 Mb); report
  4. Human HG004 (H. sapiens, genome size: 3 Gb): source of reads (Illumina pair-ends and mate-pairs) and assemblies — ABySS 2.0 studyreport
  5. Human NA12878 (H. sapiens, genome size: 3 Gb): source of reads (Illumina pair-ends and Oxford Nanopores) and assemblies — MaSuRCA blogreport

Please help us to make QUAST-LG better by sending your comments, bug reports, and suggestions to .