Fast and accurate de novo genome assembly from long uncorrected reads
Explore this paper's citation graph
Summary
It is shown that the error correction step can be omitted and high quality consensus sequences can be generated efficiently with a SIMD accelerated, partial order alignment based stand-alone consensus module called Racon, coupled with Miniasm.
- Type
- article
- Published
- 2016-08-05
- Cited by
- 2,704
- References
- 24
- Access
- Open access
- OpenAlex
- https://openalex.org/W2575750030
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:11960570
Keywords
Sequence assembly, Nanopore sequencing, Biology, Genome, Computer science
References
- Using MUMmer to Identify Similar Regions in Large Sequence Sets
- A complete bacterial genome assembled de novo using only nanopore sequencing data
- Assembling large genomes with single-molecule sequencing and locality-sensitive hashing
- Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data
- An improved algorithm for matching biological sequences.
- A fast bit-vector algorithm for approximate string matching based on dynamic programming
- Six-fold speed-up of Smith-Waterman sequence database searches using parallel processing on common microprocessors
- Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory
- Multiple sequence alignment using partial order graphs
- Generating Consensus Sequences from Partial Order Multiple Sequence Alignment Graphs
- Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences
- Fast and sensitive mapping of error-prone nanopore sequencing reads with GraphMap
- Fast and sensitive mapping of nanopore sequencing reads with GraphMap
- Evaluation of hybrid and non-hybrid methods for de novo assembly of nanopore reads
- de novo assembly and population genomic survey of natural yeast isolates with the Oxford Nanopore MinION sequencer
- Real-time selective sequencing using nanopore technology
- Edlib: a C/C ++ library for fast, exact sequence alignment using edit distance
- Phased Diploid Genome Assembly with Single Molecule Real-Time Sequencing
- Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation
- Sparc: a sparsity-based consensus algorithm for long erroneous sequencing reads
Cited by
- Genome analysis of Mycobacterium avium subspecies hominissuis strain 109
- Chromosomal level reference genome of Tachypleus tridentatus provides insights into evolution and adaptation of horseshoe crabs
- HINGE: long-read assembly achieves optimal repeat resolution
- A spectral algorithm for fast de novo layout of uncorrected long nanopore reads
- Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads
- A resource-frugal probabilistic dictionary and applications in bioinformatics
- Same-Day Diagnostic and Surveillance Data for Tuberculosis via Whole-Genome Sequencing of Direct Respiratory Samples
- Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation
- Evaluation of tools for long read RNA-seq splice-aware alignment
- Reconstructing the Gigabase Plant Genome of Solanum pennellii using Nanopore Sequencing
- From data to knowledge: The future of multi-omics data analysis for the rhizosphere
- The long reads ahead: de novo genome assembly using the MinION
- High contiguity Arabidopsis thaliana genome assembly with a single nanopore flow cell
- De novo yeast genome assemblies from MinION, PacBio and MiSeq platforms
- Fast and memory-efficient noisy read overlapping with KD-trees
- A world of opportunities with nanopore sequencing.
- Fantastic beasts and how to sequence them: genomic approaches for obscure model organisms
- Chiron: translating nanopore raw signal directly into nucleotide sequence using deep learning
- Rapid MinION metagenomic profiling of the preterm infant gut microbiota to aid in pathogen diagnostics
- De novo assembly and comparative genomics of teleosts
Related papers
- Improving the Chromosome-Level Genome Assembly of the Siamese Fighting Fish (Betta splendens) in a University Master’s Course
- Rapid de novo assembly of the European eel genome from nanopore sequencing reads
- Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes
- Rapid de novo assembly of the European eel genome from nanopore sequencing reads
- De Novo Assembly of a New Solanum pennellii Accession Using Nanopore Sequencing[CC-BY]
- Nanopore sequencing and assembly of a human genome with ultra-long reads