BUSCO Applications from Quality Assessments to Gene Prediction and Phylogenomics
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Summary
Technical sequencing quality metrics can be complemented by quantifying completeness in terms of the expected gene content of Benchmarking Universal Single-Copy Orthologs (BUSCO), now in its third release.
- Type
- article
- Published
- 2017-08-17
- Cited by
- 1,925
- References
- 48
- Access
- Open access
- OpenAlex
- https://openalex.org/W2951257985
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:4240307
Keywords
Phylogenomics, Biology, Genomics, Genome, Metagenomics
References
- RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
- Gene finding in novel genomes
- Genome Annotation and Curation Using MAKER and MAKER-P
- Eukaryotic Gene Prediction Using GeneMark.hmm-E and GeneMark-ES
- Intrahepatic Transcriptional Signature Associated with Response to Interferon-α Treatment in the Woodchuck Model of Chronic Hepatitis B
- Using geneid to Identify Genes
- Multiple molecular evidences for a living mammalian fossil
- Rodent phylogeny revised: analysis of six nuclear genes from all major rodent clades
- A network-based approach to identify substrate classes of bacterial glycosyltransferases
- A maturing understanding of the composition of the insect gene repertoire.
- OrthoDB: a hierarchical catalog of animal, fungal and bacterial orthologs
- Phylogenomics and the reconstruction of the tree of life
- Phylogenomics resolves the timing and pattern of insect evolution
- Characterization of the Kidney Transcriptome of the Long-Haired Mouse Abrothrix hirta (Rodentia, Sigmodontinae) and Comparison with That of the Olive Mouse A. olivacea
- CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes
- Finding the missing honey bee genes: lessons learned from a genome upgrade
- trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses
- Whole-genome analyses resolve early branches in the tree of life of modern birds
- Metagenomic species profiling using universal phylogenetic marker genes
- Extensive introgression in a malaria vector species complex revealed by phylogenomics
Cited by
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- Draft Genome Sequence of Amphirosellinia nigrospora JS-1675, an Endophytic Fungus from Pteris cretica
- Advances in Bioinformatics and Computational Biology: 12th Brazilian Symposium on Bioinformatics, BSB 2019, Fortaleza, Brazil, October 7–10, 2019, Revised Selected Papers
- FGMP: assessing fungal genome completeness and gene content
- De novo whole-genome assembly of a wild type yeast isolate using nanopore sequencing
- Biases in genome reconstruction from metagenomic data
- The genome of the water strider Gerris buenoi reveals expansions of gene repertoires associated with adaptations to life on the water
- Proteomics as a Metrological Tool to Evaluate Genome Annotation Accuracy Following De Novo Genome Assembly: A Case Study Using the Atlantic Bottlenose Dolphin (Tursiops truncatus)
- Rapid turnover of life-cycle-related genes in the brown algae
- Deciphering the genome and secondary metabolome of the plant pathogen Fusarium culmorum.
- Complete assembly of parental haplotypes with trio binning
- Application of High-Throughput Sequencing Methods to Spider Phylogenomics and Speciation with a Focus on the Mygalomorph Genus Aptostichus
- Genomics analysis of Aphanomyces spp. identifies a new class of oomycete effector associated with host adaptation
- De novo assembly and functional annotation of the transcriptome of Mimachlamys varia, a bioindicator marine bivalve
- NGScloud: RNA-seq analysis of non-model species using cloud computing
- Sex Determination in Ceratopteris richardii Is Accompanied by Transcriptome Changes That Drive Epigenetic Reprogramming of the Young Gametophyte
- Larval transcriptomic response to host plants in two related phytophagous lepidopteran species: implications for host specialization and species divergence
- Metabolic Capability and Phylogenetic Diversity of Mono Lake during a Bloom of the Eukaryotic Phototroph Picocystis sp. Strain ML
- Draft Genome Sequence of Muricauda sp. Strain K001 Isolated from a Marine Cyanobacterial Culture
- The genomic features of parasitism, Polyembryony and immune evasion in the endoparasitic wasp Macrocentrus cingulum
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