Genome assembly algorithms

Genome assembly algorithms are sets of well defined procedures for reconstructing DNA sequences from large numbers of shorter DNA sequence fragments. Fragments are aligned against one another and overlapping sections are identified and merged.

Latest Research and Reviews

  • Research |

    PolyGembler, a method for grouping and ordering contigs into complete pseudomolecules by combining long-read sequencing and genotype information from an outbred mapping population, improves the accuracy for assembly of polyploidy plant genomes.

    • Chenxi Zhou
    • , Bode Olukolu
    • , Dorcus C. Gemenet
    • , Shan Wu
    • , Wolfgang Gruneberg
    • , Minh Duc Cao
    • , Zhangjun Fei
    • , Zhao-Bang Zeng
    • , Andrew W. George
    • , Awais Khan
    • , G. Craig Yencho
    •  & Lachlan J. M. Coin
    Nature Genetics 52, 1256-1264
  • Research |

    Long-read metagenomics offers a valuable approach for profiling bacterial communities. This work presents a long-read assembler, metaFlye, that specifically addresses the challenges of assembling metagenomes.

    • Mikhail Kolmogorov
    • , Derek M. Bickhart
    • , Bahar Behsaz
    • , Alexey Gurevich
    • , Mikhail Rayko
    • , Sung Bong Shin
    • , Kristen Kuhn
    • , Jeffrey Yuan
    • , Evgeny Polevikov
    • , Timothy P. L. Smith
    •  & Pavel A. Pevzner
    Nature Methods 17, 1103-1110
  • Research
    | Open Access

    Accurate, phased assemblies are a key tool in understanding the human genome, particularly in highly polymorphic regions like the medically important MHC. Here the authors provide an assembly-based benchmark for this difficult-to-characterize region.

    • Chen-Shan Chin
    • , Justin Wagner
    • , Qiandong Zeng
    • , Erik Garrison
    • , Shilpa Garg
    • , Arkarachai Fungtammasan
    • , Mikko Rautiainen
    • , Sergey Aganezov
    • , Melanie Kirsche
    • , Samantha Zarate
    • , Michael C. Schatz
    • , Chunlin Xiao
    • , William J. Rowell
    • , Charles Markello
    • , Jesse Farek
    • , Fritz J. Sedlazeck
    • , Vikas Bansal
    • , Byunggil Yoo
    • , Neil Miller
    • , Xin Zhou
    • , Andrew Carroll
    • , Alvaro Martinez Barrio
    • , Marc Salit
    • , Tobias Marschall
    • , Alexander T. Dilthey
    •  & Justin M. Zook
  • Research
    | Open Access

    Haplotype reconstruction of distant genetic variants is problematic in short-read sequencing. Here, the authors describe HapTree-X, a probabilistic framework that uses differential allele-specific expression to better reconstruct paternal haplotypes from diploid and polyploid genomes.

    • Emily Berger
    • , Deniz Yorukoglu
    • , Lillian Zhang
    • , Sarah K. Nyquist
    • , Alex K. Shalek
    • , Manolis Kellis
    • , Ibrahim Numanagić
    •  & Bonnie Berger

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