Sequencing

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11th Annual <strong>Sequencing</strong>, Finishing, and Analysis in the Future Meeting TASK-DRIVEN GROWTH OF SPADES APPLICATIONS Friday, 3rd June 09:50 La Fonda Ballroom Talk (OS‐7.02) Anton Korobeynikov, Dmitry Antipov, Anton Bankevich, Elena Bushmanova, Alexey Gurevich, Alla Mikheenko, Dmitry Meleshko, Sergey Nurk, Andrey Prjibelski, Yana Safonova, Alla Lapidus, Pavel Pevzner Saint Petersburg State University Following the increased demand of the high throughput analytical software and pipelines SPAsed assembler was gradually extended into a family of SPAdes tools aimed at various sequencing technologies and applications. Metagenomics is one of the fastest developing areas of microbial research with widely spread applications such as ecology, medicine, novel natural products discovery including antibiotics, anti‐tumor and anti‐cancer agents and more. The viability of these discoveries in the majority of cases relies on the ability to produce decent assembly of a metagenome. However, the problem of accurate de novo assembly of complex metagenomics datasets is far from being solved, thus stifling the biological discoveries. The newly developed metaSPAdes is designed to fill this gap. It brings together new algorithmic ideas and proven solutions from the SPAdes toolkit to address the metagenomic assembly challenges. Plasmids harbor biomedically important genes (such as genes involved in virulence and antibiotics resistance), however there are no specialized software tools for extracting and assembling plasmid data from whole genome sequencing projects. plasmidSPAdes is another problem‐driven tool built on top of SPAdes platform to help assembling plasmids from whole genome sequencing data sets. 133
11th Annual <strong>Sequencing</strong>, Finishing, and Analysis in the Future Meeting ASSEMBLING WHOLE GENOMES FROM MIXED MICROBIAL COMMUNITIES USING HI-C Friday, 3rd June 10:10 La Fonda Ballroom Talk (OS‐7.03) Ivan Liachko 1 , Joshua Burton 1 , Laura Sycuro 2 , Andrew Wiser 2 , David Fredricks 2 , Maitreya Dunham 1 , Jay Shendure 1 1 University of Washington, 2 Fred Hutchinson Cancer Research Institute Assembly of whole genomes from next‐generation sequencing is inhibited by the lack of contiguity information in short‐read sequencing. This limitation also impedes metagenome assembly, since one cannot tell which sequences originate from the same species within a population. We have overcome these bottlenecks by adapting a chromosome conformation capture technique (Hi‐C) for the deconvolution of metagenomes and the scaffolding of de novo assemblies of individual genomes. In modeling the 3D structure of a genome, chromosome conformation capture techniques such as Hi‐C are used to measure long‐range interactions of DNA molecules in physical space. These tools employ crosslinking of chromatin in intact cells followed by intra‐molecular ligation, joining DNA fragments that were physically nearby at the time of crosslink. Subsequent deep sequencing of these DNA junctions generates a genome‐wide contact probability map that allows the 3D modeling of genomic conformation within a cell. The strong enrichment in Hi‐C signal between genetically neighboring loci allows the scaffolding of entire chromosomes from fragmented draft assemblies. Hi‐C signal also preserves the cellular origin of each DNA fragment and its interacting partner, allowing for deconvolution and assembly of multi‐chromosome genomes from a mixed population of organisms. We have used Hi‐C to scaffold whole genomes of animals, plants, fungi, as well as prokaryotes and archaea. We have also been able to use this data to annotate functional features of microbial genomes, such as centromeres in many fungal species. Additionally, we have applied our technology to diverse metagenomic populations such as craft beer, bacterial vaginosis infections, soil, and tree endophyte samples to discover and assemble the genomes of novel strains of known species as well as novel prokaryotes and eukaryotes. The high quality of Hi‐C‐based assemblies allows the simultaneous closing of numerous unculturable genomes, placement of plasmids within host genomes, and microbial strain deconvolution in a way not possible with other methods. 134
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Sequencing

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