Cargando…

Comparative genome analysis using sample-specific string detection in accurate long reads

MOTIVATION: Comparative genome analysis of two or more whole-genome sequenced (WGS) samples is at the core of most applications in genomics. These include the discovery of genomic differences segregating in populations, case-control analysis in common diseases and diagnosing rare disorders. With the...

Descripción completa

Detalles Bibliográficos
Autores principales:	Khorsand, Parsoa, Denti, Luca, Bonizzoni, Paola, Chikhi, Rayan, Hormozdiari, Fereydoun
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Oxford University Press 2021
Materias:	Original Article
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9710709/ https://www.ncbi.nlm.nih.gov/pubmed/36700094 http://dx.doi.org/10.1093/bioadv/vbab005

Ejemplares similares

Nebula: ultra-efficient mapping-free structural variant genotyper
por: Khorsand, Parsoa, et al.
Publicado: (2021)

Efficient mapping of accurate long reads in minimizer space with mapquik
por: Ekim, Bariş, et al.
Publicado: (2023)

Shark: fishing relevant reads in an RNA-Seq sample
por: Denti, Luca, et al.
Publicado: (2020)

Efficient High-Quality Metagenome Assembly from Long Accurate Reads using Minimizer-space de Bruijn Graphs
por: Benoit, Gaëtan, et al.
Publicado: (2023)

Kevlar: A Mapping-Free Framework for Accurate Discovery of De Novo Variants
por: Standage, Daniel S., et al.
Publicado: (2019)

Optimal pooling for genome re-sequencing with ultra-high-throughput short-read technologies
por: Hajirasouliha, Iman, et al.
Publicado: (2008)

Strainberry: automated strain separation in low-complexity metagenomes using long reads
por: Vicedomini, Riccardo, et al.
Publicado: (2021)

Paired-end read length lower bounds for genome re-sequencing
por: Chikhi, Rayan, et al.
Publicado: (2009)

Sketching and sampling approaches for fast and accurate long read classification
por: Das, Arun, et al.
Publicado: (2022)

MALVA: Genotyping by Mapping-free ALlele Detection of Known VAriants
por: Denti, Luca, et al.
Publicado: (2019)

TAD fusion score: discovery and ranking the contribution of deletions to genome structure
por: Huynh, Linh, et al.
Publicado: (2019)

MindTheGap: integrated detection and assembly of short and long insertions
por: Rizk, Guillaume, et al.
Publicado: (2014)

ASGAL: aligning RNA-Seq data to a splicing graph to detect novel alternative splicing events
por: Denti, Luca, et al.
Publicado: (2018)

Prediction of Neurodevelopmental Disorders Based on De Novo Coding Variation
por: Chow, Julie C., et al.
Publicado: (2022)

HapCHAT: adaptive haplotype assembly for efficiently leveraging high coverage in long reads
por: Beretta, Stefano, et al.
Publicado: (2018)

Local read haplotagging enables accurate long-read small variant calling
por: Kolesnikov, Alexey, et al.
Publicado: (2023)

Fast and accurate long-read assembly with wtdbg2
por: Ruan, Jue, et al.
Publicado: (2019)

Accurate spliced alignment of long RNA sequencing reads
por: Sahlin, Kristoffer, et al.
Publicado: (2021)

Comparing methods for constructing and representing human pangenome graphs
por: Andreace, Francesco, et al.
Publicado: (2023)

MAGI-MS: multiple seed-centric module discovery
por: Chow, Julie C, et al.
Publicado: (2022)

Triplet-based similarity score for fully multilabeled trees with poly-occurring labels
por: Ciccolella, Simone, et al.
Publicado: (2020)

MALVIRUS: an integrated application for viral variant analysis
por: Ciccolella, Simone, et al.
Publicado: (2022)

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

Compareads: comparing huge metagenomic experiments
por: Maillet, Nicolas, et al.
Publicado: (2012)

Fast and accurate long-read alignment with Burrows–Wheeler transform
por: Li, Heng, et al.
Publicado: (2010)

LoRDEC: accurate and efficient long read error correction
por: Salmela, Leena, et al.
Publicado: (2014)

Haplotype threading: accurate polyploid phasing from long reads
por: Schrinner, Sven D., et al.
Publicado: (2020)

Accurate long-read de novo assembly evaluation with Inspector
por: Chen, Yu, et al.
Publicado: (2021)

Ultra-accurate microbial amplicon sequencing with synthetic long reads
por: Callahan, Benjamin J., et al.
Publicado: (2021)

Accelerating Minimap2 for Accurate Long Read Alignment on GPUs
por: Sadasivan, Harisankar, et al.
Publicado: (2023)

Decomposing mosaic tandem repeats accurately from long reads
por: Masutani, Bansho, et al.
Publicado: (2023)

Accurate isoform discovery with IsoQuant using long reads
por: Prjibelski, Andrey D., et al.
Publicado: (2023)

Not All Scale-Free Networks Are Born Equal: The Role of the Seed Graph in PPI Network Evolution
por: Hormozdiari, Fereydoun, et al.
Publicado: (2007)

Transcriptome assembly from long-read RNA-seq alignments with StringTie2
por: Kovaka, Sam, et al.
Publicado: (2019)

Improved transcriptome assembly using a hybrid of long and short reads with StringTie
por: Shumate, Alaina, et al.
Publicado: (2022)

npInv: accurate detection and genotyping of inversions using long read sub-alignment
por: Shao, Haojing, et al.
Publicado: (2018)

Relationship between insertion/deletion (indel) frequency of proteins and essentiality
por: Chan, Simon K, et al.
Publicado: (2007)

The discovery of integrated gene networks for autism and related disorders
por: Hormozdiari, Fereydoun, et al.
Publicado: (2015)

HAT: de novo variant calling for highly accurate short-read and long-read sequencing data
por: Ng, Jeffrey K., et al.
Publicado: (2023)

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

Cannot write session to /tmp/vufind_sessions/sess_adtq1qppq61hs149qtr5ef2mc5