Cargando…

LongStitch: high-quality genome assembly correction and scaffolding using long reads

BACKGROUND: Generating high-quality de novo genome assemblies is foundational to the genomics study of model and non-model organisms. In recent years, long-read sequencing has greatly benefited genome assembly and scaffolding, a process by which assembled sequences are ordered and oriented through t...

Descripción completa

Detalles Bibliográficos
Autores principales:	Coombe, Lauren, Li, Janet X., Lo, Theodora, Wong, Johnathan, Nikolic, Vladimir, Warren, René L., Birol, Inanc
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	BioMed Central 2021
Materias:	Software
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8557608/ https://www.ncbi.nlm.nih.gov/pubmed/34717540 http://dx.doi.org/10.1186/s12859-021-04451-7

Ejemplares similares

ntEdit+Sealer: Efficient Targeted Error Resolution and Automated Finishing of Long‐Read Genome Assemblies
por: Li, Janet X., et al.
Publicado: (2022)

ARKS: chromosome-scale scaffolding of human genome drafts with linked read kmers
por: Coombe, Lauren, et al.
Publicado: (2018)

Linear time complexity de novo long read genome assembly with GoldRush
por: Wong, Johnathan, et al.
Publicado: (2023)

Tigmint: correcting assembly errors using linked reads from large molecules
por: Jackman, Shaun D., et al.
Publicado: (2018)

ntJoin: Fast and lightweight assembly-guided scaffolding using minimizer graphs
por: Coombe, Lauren, et al.
Publicado: (2020)

ARCS: scaffolding genome drafts with linked reads
por: Yeo, Sarah, et al.
Publicado: (2018)

Straglr: discovering and genotyping tandem repeat expansions using whole genome long-read sequences
por: Chiu, Readman, et al.
Publicado: (2021)

RResolver: efficient short-read repeat resolution within ABySS
por: Nikolić, Vladimir, et al.
Publicado: (2022)

LINKS: Scalable, alignment-free scaffolding of draft genomes with long reads
por: Warren, René L., et al.
Publicado: (2015)

Trycycler: consensus long-read assemblies for bacterial genomes
por: Wick, Ryan R., et al.
Publicado: (2021)

GPU acceleration of Darwin read overlapper for de novo assembly of long DNA reads
por: Ahmed, Nauman, et al.
Publicado: (2020)

ChopStitch: exon annotation and splice graph construction using transcriptome assembly and whole genome sequencing data
por: Khan, Hamza, et al.
Publicado: (2018)

Reference-free assembly of long-read transcriptome sequencing data with RNA-Bloom2
por: Nip, Ka Ming, et al.
Publicado: (2023)

Long‐read genotyping with SLANG (Simple Long‐read loci Assembly of Nanopore data for Genotyping)
por: Dorfner, Marco, et al.
Publicado: (2022)

aaHash: recursive amino acid sequence hashing
por: Wong, Johnathan, et al.
Publicado: (2023)

aaHash: recursive amino acid sequence hashing
por: Wong, Johnathan, et al.
Publicado: (2023)

Innovations and challenges in detecting long read overlaps: an evaluation of the state-of-the-art
por: Chu, Justin, et al.
Publicado: (2017)

viralFlye: assembling viruses and identifying their hosts from long-read metagenomics data
por: Antipov, Dmitry, et al.
Publicado: (2022)

Sealer: a scalable gap-closing application for finishing draft genomes
por: Paulino, Daniel, et al.
Publicado: (2015)

Ultraplexing: increasing the efficiency of long-read sequencing for hybrid assembly with k-mer-based multiplexing
por: Dilthey, Alexander T., et al.
Publicado: (2020)

SLR-superscaffolder: a de novo scaffolding tool for synthetic long reads using a top-to-bottom scheme
por: Guo, Lidong, et al.
Publicado: (2021)

LSCplus: a fast solution for improving long read accuracy by short read alignment
por: Hu, Ruifeng, et al.
Publicado: (2016)

ntHash2: recursive spaced seed hashing for nucleotide sequences
por: Kazemi, Parham, et al.
Publicado: (2022)

Assembling genomes using short-read sequencing technology
por: Jackman, Shaun D, et al.
Publicado: (2010)

HALC: High throughput algorithm for long read error correction
por: Bao, Ergude, et al.
Publicado: (2017)

LRScaf: improving draft genomes using long noisy reads
por: Qin, Mao, et al.
Publicado: (2019)

TrEMOLO: accurate transposable element allele frequency estimation using long-read sequencing data combining assembly and mapping-based approaches
por: Mohamed, Mourdas, et al.
Publicado: (2023)

TAP: a targeted clinical genomics pipeline for detecting transcript variants using RNA-seq data
por: Chiu, Readman, et al.
Publicado: (2018)

Magic-BLAST, an accurate RNA-seq aligner for long and short reads
por: Boratyn, Grzegorz M., et al.
Publicado: (2019)

Scaffolding of long read assemblies using long range contact information
por: Ghurye, Jay, et al.
Publicado: (2017)

PBHoney: identifying genomic variants via long-read discordance and interrupted mapping
por: English, Adam C, et al.
Publicado: (2014)

A new parallel pipeline for DNA methylation analysis of long reads datasets
por: Olanda, Ricardo, et al.
Publicado: (2017)

Genion, an accurate tool to detect gene fusion from long transcriptomics reads
por: Karaoglanoglu, Fatih, et al.
Publicado: (2022)

TeraStitcher - A tool for fast automatic 3D-stitching of teravoxel-sized microscopy images
por: Bria, Alessandro, et al.
Publicado: (2012)

Megabase-scale methylation phasing using nanopore long reads and NanoMethPhase
por: Akbari, Vahid, et al.
Publicado: (2021)

BugSeq: a highly accurate cloud platform for long-read metagenomic analyses
por: Fan, Jeremy, et al.
Publicado: (2021)

A graphical, interactive and GPU-enabled workflow to process long-read sequencing data
por: Reddy, Shishir, et al.
Publicado: (2021)

Identification of cell barcodes from long-read single-cell RNA-seq with BLAZE
por: You, Yupei, et al.
Publicado: (2023)

LDscaff: LD-based scaffolding of de novo genome assemblies
por: Zhao, Zicheng, et al.
Publicado: (2020)

SPAligner: alignment of long diverged molecular sequences to assembly graphs
por: Dvorkina, Tatiana, et al.
Publicado: (2020)

Cannot write session to /tmp/vufind_sessions/sess_v88ne21m03vrujp362cftphqg9