Automated Organization ProfileCenter for Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia
Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia
Current S-Index
Sum of Dataset Indices for all datasets
Average Dataset Index per Dataset
Average Dataset Index per dataset
Total Datasets
Total datasets in this organization
Average FAIR Score
Average FAIR Score per dataset
Total Citations
Total citations to the organization's datasets
Total Mentions
Total mentions of the organization's datasets
S-Index Interpretation
The S-Index (Sharing Index) is a comprehensive metric that represents the cumulative impact of all your datasets. It is calculated as the sum of Dataset Index scores across all your claimed datasets.
What it means:
- A higher S-index indicates greater overall impact of your datasets relative to typical datasets in their fields of research
- The S-Index grows as you add more datasets or as existing datasets gain more citations and mentions
- It provides a single number to track your research data impact over time
Current S-Index: 6.5 (sum of 7 datasets Dataset Index scores)
More information here.
S-Index Over Time
Cumulative Citations Over Time
Cumulative Mentions Over Time
Datasets
This repository contains benchmarking datasets and scripts for the manuscript "SPAligner: alignment of long error-prone reads to assembly graphs". Graph representation of genome assemblies has been recently used in different applications — from gene finding to haplotype separation. While many of these applications are based on aligning DNA and protein sequences to assembly graphs, existing software tools for finding such alignments have important limitations. We present a novel SPAligner (Saint Petersburg Aligner) tool for aligning long reads to assembly graphs and demonstrate that it generates accurate alignments.
Authors
- Dvorkina, Tatiana ;
- Antipov, Dmitry ;
- Korobeynikov, Anton ;
- Nurk, Sergey
This repository contains benchmarking datasets and scripts for the manuscript "SPAligner: alignment of long error-prone reads to assembly graphs". Graph representation of genome assemblies has been recently used in different applications — from gene finding to haplotype separation. While many of these applications are based on aligning DNA and protein sequences to assembly graphs, existing software tools for finding such alignments have important limitations. We present a novel SPAligner (Saint Petersburg Aligner) tool for aligning long reads to assembly graphs and demonstrate that it generates accurate alignments.
Authors
- Dvorkina, Tatiana ;
- Antipov, Dmitry ;
- Korobeynikov, Anton ;
- Nurk, Sergey
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 ofSaccharomyces cerevisiae (yeast) version R64-1-1 Caenorhabditis elegans (worm) version WBcel235Drosophila melanogaster (fruit fly) version BDGP6And de novo genome assemblies ofYeast_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 [email protected].
Authors
- Mikheenko, Alla ;
- Prjibelski, Andrey ;
- Saveliev, Vladislav ;
- Antipov, Dmitry ;
- Gurevich, Alexey
De novo genome assemblies ofYeast_PB (S. cerevisiae, genome size: 12.1 Mb): Canu, FALCON, Flye, MaSuRCA (from Illumina pair-ends and PacBio SMRT)Yeast_NP (S. cerevisiae, genome size: 12.1 Mb): Canu, Flye, MaSuRCA (from Illumina pair-ends and Oxford Nanopores)Worm_PB (C. elegans,genome size: 100.3 Mb): Canu, FALCON, Flye, MaSuRCA (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 Nanopores)Each pack 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 and other human datasets assemblies please visit http://cab.spbu.ru/software/quast-lg/ or write to [email protected].
Authors
- Mikheenko, Alla ;
- Prjibelski, Andrey ;
- Saveliev, Vladislav ;
- Antipov, Dmitry ;
- Gurevich, Alexey
Genome assemblies ofYeast_PB (S. cerevisiae, genome size: 12.1 Mb): Canu, FALCON, Flye, MaSuRCA (from Illumina pair-ends and PacBio SMRT)Yeast_NP (S. cerevisiae, genome size: 12.1 Mb): Canu, Flye, MaSuRCA (from Illumina pair-ends and Oxford Nanopores)Worm_PB (C. elegans,genome size: 100.3 Mb): Canu, FALCON, Flye, MaSuRCA (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)Each pack 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 please visit http://cab.spbu.ru/software/quast-lg/ or write to [email protected].
Authors
- Mikheenko, Alla ;
- Prjibelski, Andrey ;
- Saveliev, Vladislav ;
- Antipov, Dmitry ;
- Gurevich, Alexey
Genome assemblies ofYeast (S. cerevisiae, genome size: 12.1 Mb): ABruijn, Canu, FALCON, MaSuRCA (from Illumina pair-ends and PacBio)Worm (C. elegans,genome size: 100.3 Mb): ABruijn, Canu, FALCON, MaSuRCA (from Illumina pair-ends and PacBio)Fruit fly (D. melanogaster, genome size: 137.6 Mb): ABySS2, MaSuRCA, MEGAHIT, Meraculous, Platanus, SOAPdenovo2, SPAdes (from Illumina pair-ends and mate-pairs)Each pack is accompanied with the theoretically optimal assembly created with QUAST-LG. For more information please visit http://cab.spbu.ru/software/quast-lg/ or write to [email protected].
Authors
- Alla Mikheenko, Andrey Prjibelski
Genome assemblies ofYeast (S. cerevisiae, genome size: 12.1 Mb): ABruijn, Canu, FALCON, MaSuRCA (from Illumina pair-ends and PacBio)Worm (C. elegans,genome size: 100.3 Mb): ABruijn, Canu, FALCON, MaSuRCA (from Illumina pair-ends and PacBio)Fruit fly (D. melanogaster, genome size: 137.6 Mb): ABySS2, MaSuRCA, MEGAHIT, Meraculous, Platanus, SOAPdenovo2, SPAdes (from Illumina pair-ends and mate-pairs)Each pack is accompanied with the theoretically optimal assembly created with QUAST-LG. For more information please visit http://cab.spbu.ru/software/quast-lg/ or write to [email protected].
Authors
- Alla Mikheenko, Andrey Prjibelski