2022
Haplotype-resolved assembly of diploid genomes without parental data
Cheng H, Jarvis E, Fedrigo O, Koepfli K, Urban L, Gemmell N, Li H. Haplotype-resolved assembly of diploid genomes without parental data. Nature Biotechnology 2022, 40: 1332-1335. PMID: 35332338, PMCID: PMC9464699, DOI: 10.1038/s41587-022-01261-x.Peer-Reviewed Original Research
2021
Real-time mapping of nanopore raw signals
Zhang H, Li H, Jain C, Cheng H, Au K, Li H, Aluru S. Real-time mapping of nanopore raw signals. Bioinformatics 2021, 37: i477-i483. PMID: 34252938, PMCID: PMC8336444, DOI: 10.1093/bioinformatics/btab264.Peer-Reviewed Original ResearchConceptsRaw signalsBase-calling procedureLibrary preparation protocolState-of-the-artK-d treeSeed selection strategySupplementary dataGreen algaeTarget sequenceStreaming methodSequencing devicesGenomeSignal spaceAdapter sequencesSelection strategyChain algorithmSequenceBioinformaticsReal timeMapping accuracySignal characteristicsMapping methodRead signalSeedYeastHaplotype-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
2017
FMtree: a fast locating algorithm of FM-indexes for genomic data
Cheng H, Wu M, Xu Y. FMtree: a fast locating algorithm of FM-indexes for genomic data. Bioinformatics 2017, 34: 416-424. PMID: 28968761, DOI: 10.1093/bioinformatics/btx596.Peer-Reviewed Original ResearchConceptsFull-text indexGenomic dataState-of-the-art algorithmsMultiway treeLocation algorithmLocation operationsState-of-the-artFM-indexTree-based algorithmsPosition of patternsMemory-efficientLong textData localitySupplementary dataOccurrence positionSuffix treeSuffix arrayShort patternsAlgorithmBioinformaticsExperimental resultsTreesTextOperationTask
2015
BitMapper: an efficient all-mapper based on bit-vector computing
Cheng H, Jiang H, Yang J, Xu Y, Shang Y. BitMapper: an efficient all-mapper based on bit-vector computing. BMC Bioinformatics 2015, 16: 192. PMID: 26063651, PMCID: PMC4462005, DOI: 10.1186/s12859-015-0626-9.Peer-Reviewed Original ResearchConceptsNext-generation sequencingMapping next-generation sequencingState-of-the-art all-mappersState-of-the-artReference genomeRaw readsBit-vector algorithmMap locationBit-vectorGPL licenseEdit distanceVerification timeGenomeRunning timeData setsComputational challengesExperimental resultsIndelsHttp://homeVerificationSequenceAlgorithmMultiple locations
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