Assembly of long, error-prone reads using repeat graphs
Explore this paper's citation graph
Summary
Flye improves the speed and accuracy of genome assembly by using repeat graphs to resolve repeat regions, and nearly doubled the contiguity of the human genome assembly compared with existing assemblers.
- Type
- article
- Published
- 2018-01-12
- Cited by
- 5,028
- References
- 45
- Access
- Open access
- OpenAlex
- https://openalex.org/W2788228074
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:89616540
Keywords
Sequence assembly, Contiguity, Computer science, Hybrid genome assembly, Graph
References
- The diagram, a method for comparing sequences. Its use with amino acid and nucleotide sequences.
- Assembling large genomes with single-molecule sequencing and locality-sensitive hashing
- Chromosome dynamics in multichromosome bacteria
- Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement
- Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data
- Resolving the complexity of the human genome using single-molecule sequencing
- What is the difference between the breakpoint graph and the de Bruijn graph?
- ExSPAnder: a universal repeat resolver for DNA fragment assembly
- An Improved Method for the Microscopic Investigation of Crystals
- Ancestral reconstruction of segmental duplications reveals punctuated cores of human genome evolution
- De novo repeat classification and fragment assembly
- Matching, Euler tours and the Chinese postman
- Aggressive assembly of pyrosequencing reads with mates
- SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing
- Automated de novo identification of repeat sequence families in sequenced genomes.
- Bandage: interactive visualization of de novo genome assemblies
- The fragment assembly string graph
- Hybrid error correction and de novo assembly of single-molecule sequencing reads
- Unsupervised segmentation of continuous genomic data
- hybridSPAdes: an algorithm for hybrid assembly of short and long reads
Cited by
- Complete genome sequence of lovastatin producer Aspergillus terreus ATCC 20542 and evaluation of genomic diversity among A. terreus strains
- Complete sequence verification of plasmid DNA using the Oxford Nanopore Technologies’ MinION device
- HINGE: long-read assembly achieves optimal repeat resolution
- Recovery of gene haplotypes from a metagenome
- Integrating Hi-C links with assembly graphs for chromosome-scale assembly
- Culture-free generation of microbial genomes from human and marine microbiomes
- Long-read sequence capture of the hemoglobin gene clusters across species
- Pushing the limits of de novo genome assembly for complex prokaryotic genomes harboring very long, near identical repeats
- Versatile genome assembly evaluation with QUAST-LG
- Evaluation of Oxford Nanopore’s MinION Sequencing Device for Microbial Whole Genome Sequencing Applications
- Nanopore sequence-based genome assembly of the basmati rice
- Kermit: Guided Long Read Assembly using Coloured Overlap Graphs
- Utilization of Hybrid Assembly Approach to Determine the Genome of an Opportunistic Pathogenic Fungus, Candida albicans TIMM 1768
- A chromosome-level sequence assembly reveals the structure of the Arabidopsis thaliana Nd-1 genome and its gene set
- High-quality genome sequences of uncultured microbes by assembly of read clouds
- De novo assembly of haplotype-resolved genomes with trio binning
- New Approaches for Genome Assembly and Scaffolding.
- Long‐fragment targeted capture for long‐read sequencing of plastomes
- Comparison of long-read sequencing technologies in the hybrid assembly of complex bacterial genomes
- Assembly Graph Browser: interactive visualization of assembly graphs
Related papers
- Novo&Stitch: accurate reconciliation of genome assemblies via optical maps
- Identification of Optimum Sequencing Depth Especially for De Novo Genome Assembly of Small Genomes Using Next Generation Sequencing Data
- Efficient hybrid de novo assembly of human genomes with WENGAN
- A pilot study for channel catfish whole genome sequencing and de novo assembly
- GAGE: A critical evaluation of genome assemblies and assembly algorithms.
- Efficient algorithms for sequence assembly
- Whole-Genome Sequencing and Assembly with High-Throughput, Short-Read Technologies
- Assisted assembly: how to improve a de novo genome assembly by using related species