Topic 25

reads read sequencing genomics assembly genome nanopore reference long genomes short illumina quality sequence assemblies technologies genomic oxford assembled n50 pacbio sequenced sequences chromosome mb novo complete de length bioinformatics coverage high species repetitive chromosomes genes accurate contigs annotation whole annotated error draft accuracy variants generated contig technology hi completeness haplotype resource dna regions mapping kb busco data contiguity pipeline using bp resources coding transcriptome will genetic calling ont generation available 99 samples scaffold level scaffolds single gene copy variant comparative next alignment cost platform raw assemble generate transcripts methods gb throughput platforms contiguous scale valuable present diploid transcript pacific

481 items. Top items listed below.

Comparison of long read methods for sequencing and assembly of a plant genome 25 4

GALA: gap-free chromosome-scale assembly with long reads 25 4

Comparison of the two up-to-date sequencing technologies for genome assembly: HiFi reads of Pacbio Sequel II system and ultralong reads of Oxford Nanopore 25 4

Implications of error-prone long-read whole-genome shotgun sequencing on characterizing reference microbiomes 25 4

Telomere-to-telomere assembly of the genome of an individual Oikopleura dioica from Okinawa using Nanopore-based sequencing 25 4

A chromosome-level genome assembly for the Pacific oyster (Crassostrea gigas) 25 9 4

Long-read error correction: a survey and qualitative comparison 25 4

Complete vertebrate mitogenomes reveal widespread gene duplications and repeats 25 4

Profiling variable-number tandem repeat variation across populations using repeat-pangenome graphs 25 19 9 4

Estimating Assembly Base Errors Using K-mer Abundance Difference (KAD) Between Short Reads and Genome Assembled Sequences 25 4

HASLR: Fast Hybrid Assembly of Long Reads 25 13 4

Error correction enables use of Oxford Nanopore technology for reference-free transcriptome analysis 25 4

Highly Multiplexed Single-Cell Full-Length cDNA Sequencing of human immune cells with 10X Genomics and R2C2 25 4

First complete genome sequences of Streptococcus pyogenes NCTC 8198T and CCUG 4207T, the type strain of the type species of the genus Streptococcus: 100% match in length and sequence identity between PacBio solo and Illumina plus Oxford Nanopore hybrid assemblies 25 12 5

Optimised use of Oxford Nanopore Flowcells for Hybrid Assemblies 25 4

Whole Genome Sequences of Aedes aegypti (Linn.) Field Isolates from Southern India 48 25 9 5 4

A consensus-based ensemble approach to improve de novo transcriptome assembly 25 4

Amplification-free long read sequencing reveals unforeseen CRISPR-Cas9 off-target activity 25 4

A high-quality de novo genome assembly from a single parasitoid wasp 25 4

Extending rnaSPAdes functionality for hybridtranscriptome assembly 25 13 4

Analytical validity of nanopore sequencing for rapid SARS-CoV-2 genome analysis 25 1

Benchmarking small variant detection with ONT reveals high performance in challenging regions 25 4

Comparison of long read sequencing technologies in resolving bacteria and fly genomes 25 4

The beginning of the end: a chromosomal assembly of the New World malaria mosquito ends with a novel telomere 25 4

Chromosome-level genome assemblies of the malaria vectors Anopheles coluzzii and Anopheles arabiensis 25 4

Near-chromosome level genome assembly of the fruit pest Drosophila suzukii using long-read sequencing 25 5 4

High-quality de novo genome assembly of Kappaphycus alvarezii based on both PacBio and HiSeq sequencing 25 5 4

NanoCaller for accurate detection of SNPs and indels in difficult-to-map regions from long-read sequencing by haplotype-aware deep neural networks 25 4

Long-reads assembly of the Brassica napus reference genome, Darmor-bzh 25 4

The assembled and annotated genome of the pigeon louse Columbicola columbae, a model ectoparasite 25 4

De novo assembly of trachidermus fasciatus genome by nanopore sequencing 25 5 4

SHIMS 3.0: Highly efficient single-haplotype iterative mapping and sequencing using ultra-long nanopore reads 25 4

Chromosome-level assembly of the Caenorhabditis remanei genome reveals conserved patterns of nematode genome organization 25 21 5

A chromosome-level assembly of the black tiger shrimp (Penaeus monodon) genome facilitates the identification of novel growth-associated genes 25 9 4

Third generation indexing for third generation sequencing 25 4

Reference genome for the highly transformable Setaria viridis cultivar ME034V 25 5 4

CONSENT: Scalable long read self-correction and assembly polishing with multiple sequence alignment 25 13 4

SVJedi: Genotyping structural variations with long reads 25 13 4

LIQA: Long-read Isoform Quantification and Analysis 25 13 4

ConnectedReads: machine-learning optimized long-range genome analysis workflow for next-generation sequencing 25 4

Long-read transcriptome and other genomic resources for the angiosperm Silene noctiflora 25 5 4

Expectations and blind spots for structural variation detection from short-read alignment and long-read assembly 25 7 4

A technology-agnostic long-read analysis pipeline for transcriptome discovery and quantification 25 4

Read coverage as an indicator of misassembly in a short-read based genome assembly 25 4

AnAms1.0: A high-quality chromosome-scale assembly of a domestic cat Felis catus of American Shorthair breed 25 4

Single-molecule sequencing of long DNA molecules allows high contiguity de novo genome assembly for the fungus fly, Sciara coprophila 25 4

Real-time resolution of short-read assembly graph using ONT long reads 13 4

Targeted Transcriptome Analysis using Synthetic Long Read Sequencing Uncovers Isoform Reprograming in the Progression of Colon Cancer 25 9 4

Optimizing experimental design for genome sequencing and assembly with Oxford Nanopore Technologies 25 4

Chromosome-scale de novo diploid assembly of the apple cultivar 'Gala Galaxy' 25 4

WHOLE-GENOME SEQUENCING AND DE NOVO ASSEMBLY OF A 2019 NOVEL CORONAVIRUS (SARS-COV-2) STRAIN ISOLATED IN VIETNAM 37 25 1

Chromosome-scale assembly and annotation of the macadamia genome(Macadamia integrifolia HAES 741) 25 5

One is not enough: on the effects of reference genome for the mapping and subsequent analyses of short-reads 25 5 4

Accurate chromosome-scale haplotype-resolved assembly of human genomes 25 4

A multi-platform reference for somatic structural variation detection 25 4

Reference-free reconstruction and quantification of transcriptomes from Nanopore long-read sequencing 25 4

Investigating hospital Mycobacterium chelonae infection using whole genome sequencing and hybrid assembly 25 12 9

Third generation sequencing revises the molecular karyotype for Toxoplasma gondii and identifies emerging copy number variants in sexual recombinants. 25 4

A Rapid, Cost-Effective Tailed Amplicon Method for Sequencing SARS-CoV-2 25 1

Improving the chromosome-level genome assembly of the Siamese fighting fish (Betta splendens) in a university Master's course. 25 4

HELLO: A hybrid variant calling approach 25 4

Microbial diversity characterization of seawater in a pilot study using Oxford Nanopore Technologies long-read sequencing 25 4

A highly contiguous genome for the Golden-fronted Woodpecker (Melanerpes aurifrons) via a hybrid Oxford Nanopore and short read assembly 25 5 4

Short and Long-read Sequencing Survey of the Dynamic Transcriptomes of African Swine Fever Virus and its Host 25 4

Demonstrating the utility of flexible sequence queries against indexed short reads with FlexTyper 25 13 4

A Phased Canis lupus familiaris Labrador Retriever Reference Genome Utilizing High Molecular Weight DNA Extraction Methods and High Resolution Sequencing Technologies 25 4

Chromosome-scale assembly of the genome of Salix dunnii reveals a male-heterogametic sex determination system on chromosome 7 25 5

RefKA: A fast and efficient long-read genome assembly approach for large and complex genomes 25 13 4

Complete and haplotype-specific sequence assembly of segmental duplication-mediated genome rearrangements using targeted CRISPR-targeted ultra-long read sequencing (CTLR-Seq) 25 9 4

Kmer2SNP: reference-free SNP calling from raw reads based on matching 13 4

A haplotype-resolved, de novo genome assembly for the wood tiger moth (Arctia plantaginis) through trio binning 25 5 4

Direct nanopore sequencing of mRNA reveals landscape of transcript isoforms in apicomplexan parasites 25 9 4

De Novo Assembly of a Chromosome-Scale Reference Genome for the Northern Flicker Colaptes auratus 25 5 4

Improved reference genome uncovers novel sex-linked regions in the guppy (Poecilia reticulata) 25 21 5 4

A workflow for accurate metabarcoding using nanopore MinION sequencing 125 25 4

MINTIE: identifying novel structural and splice variants in transcriptomes using RNA-seq data 97 25 9 4

Refinement of Genome assemblies of Pigeonpea (Cajanus cajan) 25 4

Chromosome-level genome assembly of a benthic associated Syngnathiformes species: the common dragonet, Callionymus lyra 25 5 4

Liftoff: an accurate gene annotation mapping tool 13 4

Overcoming uncollapsed haplotypes in long-read assemblies of non-model organisms 25 4

Long-read sequencing reveals widespread intragenic structural variants in a recent allopolyploid crop plant 25 5 4

Phylogenetic placement of short reads without sequence alignment 140 25 4

QAlign: Aligning nanopore reads accurately using current-level modeling 25 13 4

Combined short and long-read sequencing reveals a complex transcriptomic architecture of African swine fever virus 25 9 4

Advancing the genetic utility of pre-clinical species through a high-quality assembly of the cynomolgus monkey (Macaca fascicularis) genome 25 4

Ratatosk - Hybrid error correction of long reads enables accurate variant calling and assembly 25 4

An integrated personal and population-based Egyptian genome reference 25 19 4

High accuracy DNA sequencing on a small, scalable platform via electrical detection of single base incorporations 25 4

Complete and validated genomes from a metagenome 25 4

A strategy for complete telomere-to-telomere assembly of ciliate macronuclear genome using ultra-high coverage Nanopore data 25 4

Sensitive alignment using paralogous sequence variants improves long read mapping and variant calling in segmental duplications 25 4

Genome sequence analysis of a giant-rooted 'Sakurajima daikon' radish (Raphanus sativus) 25 9 4

Probabilistic Approach to Understand Errors in Sequencing and its based Applications 145 4

Insights into dispersed duplications and complex structural mutations from whole genome sequencing 706 families 97 19 4

Complete representation of a tapeworm genome reveals chromosomes capped by centromeres, necessitating a dual role in segregation and protection 25 5

De novo genome assembly and transcriptome analysis for the drought and salt resistant Solanum sitiens 25 9 4

Extensive genomic and transcriptomic variation defines the chromosome-scale assembly of Haemonchus contortus, a model gastrointestinal worm 25 9 5

A short read de novo transcriptome construction pipeline optimized by long reads reveals novel developmentally regulated gene isoforms and disease targets in hundreds of eye samples 25 9 4

Long-read shotgun metagenome sequencing using PromethION uncovers novel bacteriophages, their abundance, and interaction with host bacterial immunity in the oral microbiota 25 12 5 4

I-CONVEX: Fast and Accurate de Novo Transcriptome Recovery from Long Reads 25 4