2022
Metagenome assembly of high-fidelity long reads with hifiasm-meta
Feng X, Cheng H, Portik D, Li H. Metagenome assembly of high-fidelity long reads with hifiasm-meta. Nature Methods 2022, 19: 671-674. PMID: 35534630, PMCID: PMC9343089, DOI: 10.1038/s41592-022-01478-3.Peer-Reviewed Original Research
2021
Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm
Cheng H, Concepcion G, Feng X, Zhang H, Li H. Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm. Nature Methods 2021, 18: 170-175. PMID: 33526886, PMCID: PMC7961889, DOI: 10.1038/s41592-020-01056-5.Peer-Reviewed Original ResearchConceptsHaplotype-resolved de novo assembliesAssembly graphStudy of sequence variationHaplotype-resolved assembliesDe novo assemblyGraph-based assemblersConsensus copyHaplotype informationSequence readsHexaploid genomeTrio binningSequence variationHifiasmHeterozygous allelesHaplotypesGenomeCalifornia redwoodBinning algorithmAssemblyHexaploidAllelesCopy
2018
Comprehensive transcriptome analysis of Sarcophaga peregrina, a forensically important fly species
Kim J, Lim H, Shin S, Cha H, Seo J, Kim S, Park S, Son G. Comprehensive transcriptome analysis of Sarcophaga peregrina, a forensically important fly species. Scientific Data 2018, 5: 180220. PMID: 30398471, PMCID: PMC6219405, DOI: 10.1038/sdata.2018.220.Peer-Reviewed Original ResearchConceptsGenome informationSarcophaga peregrinaFly speciesSequence informationS. peregrinaComprehensive transcriptome analysisPrecise sequence informationDe novo assemblyMinimal postmortem intervalImportant fly speciesPrimary sequence informationGene expression datasetsFunctional annotationGenome databaseNovo assemblyTranscriptome analysisGene OntologyKyoto EncyclopediaRaw readsRNA sequencingRNA transcriptsIllumina MiSeqExpression datasetsForensic importanceUnigenes
2016
De Novo Genome Assembly Shows Genome Wide Similarity between Trypanosoma brucei brucei and Trypanosoma brucei rhodesiense
Sistrom M, Evans B, Benoit J, Balmer O, Aksoy S, Caccone A. De Novo Genome Assembly Shows Genome Wide Similarity between Trypanosoma brucei brucei and Trypanosoma brucei rhodesiense. PLOS ONE 2016, 11: e0147660. PMID: 26910229, PMCID: PMC4766357, DOI: 10.1371/journal.pone.0147660.Peer-Reviewed Original ResearchConceptsGenome assemblyGenetic recombinationT. bruceiPentatricopeptide repeat-containing proteinGenome-wide similarityDe novo genome assemblyHybrid de novo assemblyComparative genomic analysisRepeat-containing proteinVariant surface glycoprotein (VSG) coatComplete genome assemblyDe novo assemblyNovo genome assemblyGenomic differentiationSignificant epidemiological consequencesWhole-genome sequencingGene familyPutative genesEukaryotic pathogensNovo assemblySerum resistance associated geneHuman infective strainsGenomic analysisSingle geneAlcohol oxidoreductase
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