BUSCO Update: Novel and Streamlined Workflows along with Broader and Deeper Phylogenetic Coverage for Scoring of Eukaryotic, Prokaryotic, and Viral Genomes

Molecular Biology and Evolution, Год журнала: 2021, Номер 38(10), С. 4647 - 4654

Опубликована: Июль 25, 2021

Abstract Methods for evaluating the quality of genomic and metagenomic data are essential to aid genome assembly procedures correctly interpret results subsequent analyses. BUSCO estimates completeness redundancy processed based on universal single-copy orthologs. Here, we present new functionalities major improvements software, as well renewal expansion underlying sets in sync with OrthoDB v10 release. Among novelties, now enables phylogenetic placement input sequence automatically select most appropriate set assessment, allowing analysis metagenome-assembled genomes unknown origin. A newly introduced workflow increases efficiency runtimes especially large eukaryotic genomes. is only tool capable assessing both prokaryotic species, can be applied various types, from assemblies bins, transcriptomes gene sets.

Язык: Английский

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dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication

The ISME Journal, Год журнала: 2017, Номер 11(12), С. 2864 - 2868

Опубликована: Июль 25, 2017

Язык: Английский

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Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

Nature Biotechnology, Год журнала: 2017, Номер 35(8), С. 725 - 731

Опубликована: Авг. 1, 2017

We present two standards developed by the Genomic Standards Consortium (GSC) for reporting bacterial and archaeal genome sequences. Both are extensions of Minimum Information about Any (x) Sequence (MIxS). The a Single Amplified Genome (MISAG) Metagenome-Assembled (MIMAG), including, but not limited to, assembly quality, estimates completeness contamination. These can be used in combination with other GSC checklists, including (MIGS), Metagenomic (MIMS), Marker Gene (MIMARKS). Community-wide adoption MISAG MIMAG will facilitate more robust comparative genomic analyses diversity.

Язык: Английский

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Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life

Nature Microbiology, Год журнала: 2017, Номер 2(11), С. 1533 - 1542

Опубликована: Сен. 11, 2017

Abstract Challenges in cultivating microorganisms have limited the phylogenetic diversity of currently available microbial genomes. This is being addressed by advances sequencing throughput and computational techniques that allow for cultivation-independent recovery genomes from metagenomes. Here, we report reconstruction 7,903 bacterial archaeal >1,500 public All are estimated to be ≥50% complete nearly half ≥90% with ≤5% contamination. These increase genome trees >30% provide first representatives 17 three candidate phyla. We also recovered 245 Patescibacteria superphylum (also known as Candidate Phyla Radiation) find relative this group varies substantially different protein marker sets. The scale quality data set demonstrate recovering metagenomes provides an expedient path forward exploring dark matter.

Язык: Английский

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BlobToolKit – Interactive Quality Assessment of Genome Assemblies

G3 Genes Genomes Genetics, Год журнала: 2020, Номер 10(4), С. 1361 - 1374

Опубликована: Фев. 19, 2020

Reconstruction of target genomes from sequence data produced by instruments that are agnostic as to the species-of-origin may be confounded contaminant DNA. Whether introduced during sample processing or through co-extraction alongside DNA, if insufficient care is taken assembly process, final assembled genome a mixture several species. Such assemblies can confound sequence-based biological inference and, when deposited in public databases, included downstream analyses users unaware underlying problems. We present BlobToolKit, software suite aid researchers identifying and isolating non-target draft publicly available assemblies. BlobToolKit used process assembly, read analysis files for fully reproducible interactive exploration browser-based Viewer. filter helping produce with high credibility. have been running an automated pipeline on eukaryotic International Nucleotide Sequence Data Collaboration making results instance Viewer at https://blobtoolkit.genomehubs.org/view aim complete all then maintain currency flow new genomes. worked embed these views into presentation European Archive, providing indication quality record links out allow full

Язык: Английский

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Shotgun metagenomics, from sampling to analysis

Nature Biotechnology, Год журнала: 2017, Номер 35(9), С. 833 - 844

Опубликована: Сен. 1, 2017

Язык: Английский

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Best practices for analysing microbiomes

Nature Reviews Microbiology, Год журнала: 2018, Номер 16(7), С. 410 - 422

Опубликована: Май 23, 2018

Язык: Английский

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Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle

Cell, Год журнала: 2019, Номер 176(3), С. 649 - 662.e20

Опубликована: Янв. 1, 2019

The body-wide human microbiome plays a role in health, but its full diversity remains uncharacterized, particularly outside of the gut and international populations. We leveraged 9,428 metagenomes to reconstruct 154,723 microbial genomes (45% high quality) spanning body sites, ages, countries, lifestyles. recapitulated 4,930 species-level genome bins (SGBs), 77% without public repositories (unknown SGBs [uSGBs]). uSGBs are prevalent (in 93% well-assembled samples), expand underrepresented phyla, enriched non-Westernized populations (40% total SGBs). annotated 2.85 M genes SGBs, many associated with conditions including infant development (94,000) or Westernization (106,000). permit deeper analyses increase average mappability metagenomic reads from 67.76% 87.51% (median 94.26%) 65.14% 82.34% mouth. thus identify thousands yet-to-be-named species, pangenomes human-associated microbes, allow better exploitation technologies.

Язык: Английский

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Significantly improving the quality of genome assemblies through curation

GigaScience, Год журнала: 2021, Номер 10(1)

Опубликована: Янв. 1, 2021

Abstract Genome sequence assemblies provide the basis for our understanding of biology. Generating error-free is therefore ultimate, but sadly still unachieved goal a multitude research projects. Despite ever-advancing improvements in data generation, assembly algorithms and pipelines, no automated approach has so far reliably generated near genome eukaryotes. Whilst working towards improved datasets fully evaluation curation actively used to bridge this shortcoming significantly reduce number errors. In addition increase product value, insights gained from are fed back into strategy contribute notable quality. We describe tried tested using gEVAL, browser. outline procedures applied gEVAL also recommendations gEVAL-independent context facilitate uptake wider community.

Язык: Английский

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Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system

Nature Communications, Год журнала: 2016, Номер 7(1)

Опубликована: Окт. 24, 2016

Abstract The subterranean world hosts up to one-fifth of all biomass, including microbial communities that drive transformations central Earth’s biogeochemical cycles. However, little is known about how complex in such environments are structured, and inter-organism interactions shape ecosystem function. Here we apply terabase-scale cultivation-independent metagenomics aquifer sediments groundwater, reconstruct 2,540 draft-quality, near-complete complete strain-resolved genomes represent the majority bacterial phyla as well 47 newly discovered phylum-level lineages. Metabolic analyses spanning this vast phylogenetic diversity representing 36% organisms detected system used document distribution pathways coexisting organisms. Consistent with prior findings indicating metabolic handoffs simple consortia, find few within community can conduct multiple sequential redox transformations. As environmental conditions change, different assemblages selected for, altering linkages among major

Язык: Английский

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