The ELIXIR Human Copy Number Variations Community:building bioinformatics infrastructure for research

Copy number variations (CNVs) are major causative contributors both in the genesis of genetic diseases and human neoplasias. While 'High-Throughput' sequencing technologies are increasingly becoming the primary choice for genomic screening analysis, their ability to efficiently detect CNVs is still heterogeneous and remains to be developed. The aim of this white paper is to provide a guiding framework for the future contributions of ELIXIR's recently established h uman CNV Community, with implications beyond human disease diagnostics and population genomics. This white paper is the direct result of a strategy meeting that took place in September 2018 in Hinxton (UK) and involved representatives of 11 ELIXIR Nodes. The meeting led to the definition of priority objectives and tasks, to address a wide range of CNV-related challenges ranging from detection and interpretation to sharing and training. Here, we provide suggestions on how to align these tasks within the ELIXIR Platforms strategy, and on how to frame the activities of this new ELIXIR Community in the international context

Roadmap Towards Communitywide Intercalibration and Standardization of Ocean Nucleic Acids ‘Omics Measurements

In January 2020, the US Ocean Carbon & Biogeochemistry (OCB) Project Office funded the Ocean Nucleic Acids 'omics Intercalibration and Standardization workshop held at the University of North Carolina in Chapel Hill. Thirty-two participants from across the US, along with guests from Canada and France, met to develop a framework for standardization and intercalibration (S&I) of ocean nucleic acid ‘omics (na’omics) approaches (i.e., amplicon sequencing, metagenomics and metatranscriptomics). During the three-day workshop, participants discussed numerous topics, including: a) sample biomass collection and nucleic acid preservation for downstream analysis, b) extraction protocols for nucleic acids, c) addition of standard reference material to nucleic acid isolation protocols, d) isolation methods unique to RNA, e) sequence library construction, and f ) integration of bioinformatic considerations. This report provides a summary of these and other topics covered during the workshop and a series of recommendations for future S&I activities for na’omics approaches.The Ocean Nucleic Acids ‘Omics Intercalibration and Standardization Workshop was supported by grants from the Ocean Carbon & Biogeochemistry Program (OCB) – funding provided by the National Science Foundation (NSF) and the National Aeronautics and Space Administration (NASA) – and the Simons Foundation. This report was developed with federal support of NSF (OCE-1558412) and NASA (NNX17AB17G)

Targeted Computational Approaches for Mining Functional Elements in Metagenomes

Thesis (Ph.D.) - Indiana University, Informatics, 2012Metagenomics enables the genomic study of uncultured microorganisms by directly extracting the genetic material from microbial communities for sequencing. Fueled by the rapid development of Next Generation Sequencing (NGS) technology, metagenomics research has been revolutionizing the field of microbiology, revealing the taxonomic and functional composition of many microbial communities and their impacts on almost every aspect of life on Earth. Analyzing metagenomes (a metagenome is the collection of genomic sequences of an entire microbial community) is challenging: metagenomic sequences are often extremely short and therefore lack genomic contexts needed for annotating functional elements, while whole-metagenome assemblies are often poor because a metagenomic dataset contains reads from many different species. Novel computational approaches are still needed to get the most out of the metagenomes. In this dissertation, I first developed a binning algorithm (AbundanceBin) for clustering metagenomic sequences into groups, each containing sequences from species of similar abundances. AbundanceBin provides accurate estimations of the abundances of the species in a microbial community and their genome sizes. Application of AbundanceBin prior to assembly results in better assemblies of metagenomes--an outcome crucial to downstream analyses of metagenomic datasets. In addition, I designed three targeted computational approaches for assembling and annotating protein coding genes and other functional elements from metagenomic sequences. GeneStitch is an approach for gene assembly by connecting gene fragments scattered in different contigs into longer genes with the guidance of reference genes. I also developed two specialized assembly methods: the targeted-assembly method for assembling CRISPRs (Clustered Regularly Interspersed Short Palindromic Repeats), and the constrained-assembly method for retrieving chromosomal integrons. Applications of these methods to the Human Microbiome Project (HMP) datasets show that human microbiomes are extremely dynamic, reflecting the interactions between community members (including bacteria and viruses)

A Beginner’s Guide on Integrating *Omics Approaches to Study Marine Microbial Communities: Details and Discussions From Sample Collection to Bioinformatics Analysis

The variety of Earth’s organisms is manifold. However, it is the small-scale marine community that makes the world goes round. Microbial organisms of pro- and eukaryotic origin drive the carbon supply and nutrient cycling, thus are mediating the primary productivity within the world largest ecosystem called ocean. But due to the ocean’s great size and large number of biogeographically habitats, the total of microbial species can hardly be grabbed and therefore their functional roles not fully described. However, recent advances in high-throughput sequencing technologies are revolutionizing our understanding of the marine microbial diversity, ecology and evolution. Nowadays, research questions on species differentiation can be solved with genomic approaches such as metabarcoding, while transcriptomics offers the possibility to assign gene functions even to a single cell, e.g., single-cell transcriptomics. On the other hand, due to the diversified amount of sequencing data, the certainty of a data crisis is currently evolving. Scientists are forced to broaden their view on bioinformatics resources for analysis and data storage in from of, e.g., cloud services, to ensure the data’s exchangeability. Which is why time resources are now shifting toward solving data problems rather than answering the eco-evolutionary questions stated in the first place. This review is intended to provide exchange on *omics approaches and key points for discussions on data handling used to decipher the relevant diversity and functions of microbial organisms in the marine ecosystem

US National BioGeoSCAPES Workshop Report

Virtual Meeting held November 10-12, 2021BioGeoSCAPES (BGS) is an international program being developed to understand controls on ocean productivity and metabolism by integrating systems biology (‘omics) and biogeochemistry (Figure 1). To ensure global input into the design of the BGS Program, countries interested in participating were tasked with holding an organizing meeting to discuss the country-specific research priorities. A United States BGS planning meeting, sponsored by the Ocean Carbon & Biogeochemistry (OCB) Project Office, was convened virtually November 10-12, 2021. The objectives of the meeting were to communicate the planning underway by international partners, engage the US community to explore possible national contributions to such a program, and build understanding, support, and momentum for US efforts towards BGS. The meeting was well-attended, with 154 participants and many fruitful discussions that are summarized in this document. Key outcomes from the meeting were the identification of additional programs and partners for BGS, a prioritization of measurements requiring intercalibration, and the development of a consensus around key considerations to be addressed in a science plan. Looking forward, the hope is that this workshop will serve as the foundation for future US and international discussions and planning for a BGS program, enabled by NSF funding for an AccelNet project (AccelNet - Implementation: Development of an International Network for the Study of Ocean Metabolism and Nutrient Cycles on a Changing Planet (BioGeoSCAPES)), beginning in 2022.This workshop was held thanks to funding to US OCB by the National Science Foundation (NSF) (OCE-1850983) and National Aeronautic and Space Administration (NASA) (NNX17AB17G). The organizers give thanks to all workshop participants for their thoughtful discussions and input during the workshop

From barcoding to metagenomics: molecular identification techniques for ecological studies of endangered primates

DNA markers are increasingly used for studying the taxonomic composition of environmental samples that contain DNA from different species. Here, I demonstrate that some of the currently used identification techniques based on K2P are flawed and reveal that DNA barcode species coverage for Metazoa in open-access databases remains poor. I then test based on existing and newly generated barcodes whether metabarcoding or metagenomics should be used for studying the DNA in primate fecal samples. I conclude that the latter is preferable because it simultaneously provides information on diet, host genetics, and parasite loads. In addition, newly developed read-based identification strategies reveal that metagenomic data provide more taxonomic precision for plant species than the barcodes used in metabarcoding. However, metabarcoding may be useful for diet quantification given that read counts are correlated between metabarcoding and metagenomic datasets for the same samples.Open Acces