Ivan Sović
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Assembly and annotation of 2 high-quality columbid reference genomes from sequencing of a <i>Columba livia</i> × <i>Columba guinea</i> F1 hybrid Open
Pigeons and doves (family Columbidae) are one of the most diverse extant avian lineages, and many species have served as key models for evolutionary genomics, developmental biology, physiology, and behavioral studies. Building genomic reso…
Assembly and annotation of two high-quality columbid reference genomes from sequencing of a <i>Columba livia</i> x <i>Columba guinea</i> F <sub>1</sub> hybrid Open
Pigeons and doves (family Columbidae) are one of the most diverse extant avian lineages, and many species have served as key models for evolutionary genomics, developmental biology, physiology, and behavioral studies. Building genomic reso…
View article: The complete sequence of a human genome
The complete sequence of a human genome Open
Since its initial release in 2000, the human reference genome has covered only the euchromatic fraction of the genome, leaving important heterochromatic regions unfinished. Addressing the remaining 8% of the genome, the Telomere-to-Telomer…
Chasing perfection: validation and polishing strategies for telomere-to-telomere genome assemblies Open
Advances in long-read sequencing technologies and genome assembly methods have enabled the recent completion of the first Telomere-to-Telomere (T2T) human genome assembly, which resolves complex segmental duplications and large tandem repe…
Chasing perfection: validation and polishing strategies for telomere-to-telomere genome assemblies Open
Advances in long-read sequencing technologies and genome assembly methods have enabled the recent completion of the first Telomere-to-Telomere (T2T) human genome assembly, which resolves complex segmental duplications and large tandem repe…
The complete sequence of a human genome Open
In 2001, Celera Genomics and the International Human Genome Sequencing Consortium published their initial drafts of the human genome, which revolutionized the field of genomics. While these drafts and the updates that followed effectively …
View article: Towards complete and error-free genome assemblies of all vertebrate species
Towards complete and error-free genome assemblies of all vertebrate species Open
High-quality and complete reference genome assemblies are fundamental for the application of genomics to biology, disease, and biodiversity conservation. However, such assemblies are only available for a few non-microbial species 1–4 . To …
Graphmap2 - splice-aware RNA-seq mapper for long reads Open
In this paper we present Graphmap2, a splice-aware mapper built on our previously developed DNA mapper Graphmap. Graphmap2 is tailored for long reads produced by Pacific Biosciences and Oxford Nanopore devices. It uses several newly develo…
RNA Transcriptome Mapping with GraphMap Open
Next generation sequencing technologies have made RNA sequencing widely accessible and applicable in many areas of research. In recent years, 3rd generation sequencing technologies have matured and are slowly replacing NGS for DNA sequenci…
Fast and accurate de novo genome assembly from long uncorrected reads Open
The assembly of long reads from Pacific Biosciences and Oxford Nanopore Technologies typically requires resource-intensive error-correction and consensus-generation steps to obtain high-quality assemblies. We show that the error-correction…
Fast and accurate <i>de novo</i> genome assembly from long uncorrected reads Open
The assembly of long reads from Pacific Biosciences and Oxford Nanopore Technologies typically requires resource intensive error correction and consensus generation steps to obtain high quality assemblies. We show that the error correction…
Evaluation of hybrid and non-hybrid methods for <i>de novo</i> assembly of nanopore reads Open
Motivation : Recent emergence of nanopore sequencing technology set a challenge for established assembly methods. In this work, we assessed how existing hybrid and non-hybrid de novo assembly methods perform on long and error prone nanopor…
Fast and sensitive mapping of nanopore sequencing reads with GraphMap Open
Realizing the democratic promise of nanopore sequencing requires the development of new bioinformatics approaches to deal with its specific error characteristics. Here we present GraphMap, a mapping algorithm designed to analyse nanopore s…
Algorithms for de novo genome assembly from third generation sequencing data Open
During the past ten years, genome sequencing has been an extremely hot and active topic, with an especial momentum happening right now. New, exciting and more affordable technologies have been released, requiring the rapid development of n…