This is a limited proof of concept to search for research data, not a production system.

Search the MIT Libraries

Title: Genome assemblies for "Versatile genome assembly evaluation with QUAST-LG"

Type Dataset Alla Mikheenko, Andrey Prjibelski, Vladislav Saveliev, Dmitry Antipov, Alexey Gurevich (2018): Genome assemblies for "Versatile genome assembly evaluation with QUAST-LG". Zenodo. Dataset. https://zenodo.org/record/1240963

Authors: Alla Mikheenko (Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia) ; Andrey Prjibelski (Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia) ; Vladislav Saveliev (Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia) ; Dmitry Antipov (Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia) ; Alexey Gurevich (Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia) ;

Links

Summary

Supplementary data for A. Mikheenko, A. Prjibelski, V. Saveliev, D. Antipov, A. Gurevich. Versatile genome assembly evaluation with QUAST-LG. ISMB 2018 PROCEEDINGS (Bioinformatics journal)

Reference genomes of

Saccharomyces cerevisiae (yeast) version R64-1-1  Caenorhabditis elegans (worm) version WBcel235 Drosophila melanogaster (fruit fly) version BDGP6

And de novo genome assemblies of

Yeast_PB (S. cerevisiae, genome size: 12.1 Mb): Canu, FALCON, Flye, MaSuRCA, Miniasm (from Illumina pair-ends and PacBio SMRT) Yeast_NP (S. cerevisiae, genome size: 12.1 Mb): Canu, Flye, MaSuRCA, Miniasm (from Illumina pair-ends and Oxford Nanopore) Worm_PB (C. elegans, genome size: 100.3 Mb): Canu, FALCON, Flye, MaSuRCA, Miniasm (from Illumina pair-ends and PacBio SMRT) Fly_MP (D. melanogaster, genome size: 137.6 Mb): ABySS2, MaSuRCA, Meraculous, Platanus, SOAPdenovo2, SPAdes (from Illumina pair-ends and mate-pairs) Human_MP (H. sapiens, genome size: 3.1 Gb): UpperBound assembly only (from Illumina pair-ends and mate-pairs) Human_NP (H. sapiens, genome size: 3.1 Gb): UpperBound assembly only (from Illumina pair-ends and Oxford Nanopore)

Each pack (items 1-4) is accompanied with the upper bound assembly created with QUAST-LG (for computing theoretical limits on assembly correctness and completeness for a particular genome and set of reads). For more information, interactive QUAST-LG reports, and links to de novo assemblies of the human datasets please visit http://cab.spbu.ru/software/quast-lg/ or write to quast.support@cab.spbu.ru.

More information

  • DOI: 10.5281/zenodo.1240963
  • Language: en

Subjects

  • genome assembly, genome assembly evaluation

Dates

  • Publication date: 2018
  • Issued: April 02, 2018

Rights

Much of the data past this point we don't have good examples of yet. Please share in #rdi slack if you have good examples for anything that appears below. Thanks!

Format

electronic resource

Relateditems

DescriptionItem typeRelationshipUri
IsDocumentedByhttp://cab.spbu.ru/software/quast-lg/
IsVersionOfhttps://doi.org/10.5281/zenodo.1050295
IsPartOfhttps://zenodo.org/communities/zenodo