Dataset Information

FGMP: assessing fungal genome completeness.

ABSTRACT: BACKGROUND:Inexpensive high-throughput DNA sequencing has democratized access to genetic information for most organisms so that research utilizing a genome or transcriptome of an organism is not limited to model systems. However, the quality of the assemblies of sampled genomes can vary greatly which hampers utility for comparisons and meaningful interpretation. The uncertainty of the completeness of a given genome sequence can limit feasibility of asserting patterns of high rates of gene loss reported in many lineages. RESULTS:We propose a computational framework and sequence resource for assessing completeness of fungal genomes called FGMP (Fungal Genome Mapping Project). Our approach is based on evolutionary conserved sets of proteins and DNA elements and is applicable to various types of genomic data. We present a comparison of FGMP and state-of-the-art methods for genome completeness assessment utilizing 246 genome assemblies of fungi. We discuss genome assembly improvements/degradations in 57 cases where assemblies have been updated, as recorded by NCBI assembly archive. CONCLUSION:FGMP is an accurate tool for quantifying level of completion from fungal genomic data. It is particularly useful for non-model organisms without reference genomes and can be used directly on unassembled reads, which can help reducing genome sequencing costs.

SUBMITTER: Cisse OH

PROVIDER: S-EPMC6466665 | biostudies-literature | 2019 Apr

REPOSITORIES: biostudies-literature

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FGMP: assessing fungal genome completeness.

Cissé Ousmane H OH Stajich Jason E JE

BMC bioinformatics 20190415 1

<h4>Background</h4>Inexpensive high-throughput DNA sequencing has democratized access to genetic information for most organisms so that research utilizing a genome or transcriptome of an organism is not limited to model systems. However, the quality of the assemblies of sampled genomes can vary greatly which hampers utility for comparisons and meaningful interpretation. The uncertainty of the completeness of a given genome sequence can limit feasibility of asserting patterns of high rates of gen ...[more]

PMID: 30987585

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Project description:BackgroundDuring health emergencies, leading healthcare organisations, such as the World Health Organization (WHO), the European Centre for Disease Control and Prevention (ECDC), and the United States Centers for Disease Control and Prevention (CDC), provide guidance for public health response. Previous studies have evaluated clinical practice guidelines (CPGs) produced in response to epidemics or pandemics, yet few have focused on public health guidelines and recommendations. To address this gap, we assessed health systems guidance (HSG) produced by the WHO, the ECDC, and the CDC for the 2009 H1N1 and COVID-19 pandemics.MethodsWe extracted HSG for the H1N1 and COVID-19 pandemics from the organisations' dedicated repositories and websites. After screening the retrieved documents for eligibility, five assessors evaluated them using the Appraisal of Guidelines Research & Evaluation - Health Systems (AGREE-HS) tool to assess the completeness and transparency of reporting according to the five AGREE-HS domains: "Topic", "Participants", "Methods", "Recommendations", and "Implementability".ResultsFollowing the screening process, we included 108 HSG in the analysis. We observed statistically significant differences between the H1N1 and COVID-19 pandemics, with HSG issued during COVID-19 receiving higher AGREE-HS scores. The HSG produced by the CDC had significantly lower overall scores and single-domain scores compared to the WHO and ECDC. However, all HSG scored relatively low, under the median of 40 total points (range = 10-70), indicating incomplete reporting. The HSG produced by all three organisations received a median score <4 (range = 1-7) for the "Participants", "Methods", and "Implementability" domains.ConclusionsThere is still significant progress to be made in the quality and completeness of reporting in HSG issued during pandemics, especially regarding methodological approaches and the composition of the guidance development team. Due to their significant impact and importance for healthcare systems globally, HSG issued during future healthcare crises should adhere to best reporting practices to increase uptake by stakeholders and ensure public trust in healthcare organisations.

Dataset Information

FGMP: assessing fungal genome completeness.

Publications

FGMP: assessing fungal genome completeness.

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