Cargando…

Comprehensive benchmarking of software for mapping whole genome bisulfite data: from read alignment to DNA methylation analysis

Whole genome bisulfite sequencing is currently at the forefront of epigenetic analysis, facilitating the nucleotide-level resolution of 5-methylcytosine (5mC) on a genome-wide scale. Specialized software have been developed to accommodate the unique difficulties in aligning such sequencing reads to...

Descripción completa

Detalles Bibliográficos
Autores principales:	Nunn, Adam, Otto, Christian, Stadler, Peter F, Langenberger, David
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Oxford University Press 2021
Materias:	Method Review
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8425420/ https://www.ncbi.nlm.nih.gov/pubmed/33624017 http://dx.doi.org/10.1093/bib/bbab021

Ejemplares similares

Erratum to: Comprehensive benchmarking of software for mapping whole genome bisulfite data: from read alignment to DNA methylation analysis
por: Nunn, Adam, et al.
Publicado: (2021)

Manipulating base quality scores enables variant calling from bisulfite sequencing alignments using conventional bayesian approaches
por: Nunn, Adam, et al.
Publicado: (2022)

BSmooth: from whole genome bisulfite sequencing reads to differentially methylated regions
por: Hansen, Kasper D, et al.
Publicado: (2012)

BatMeth: improved mapper for bisulfite sequencing reads on DNA methylation
por: Lim, Jing-Quan, et al.
Publicado: (2012)

GBSA: a comprehensive software for analysing whole genome bisulfite sequencing data
por: Benoukraf, Touati, et al.
Publicado: (2013)

Benchmarking DNA methylation analysis of 14 alignment algorithms for whole genome bisulfite sequencing in mammals
por: Gong, Wentao, et al.
Publicado: (2022)

metilene: fast and sensitive calling of differentially methylated regions from bisulfite sequencing data
por: Jühling, Frank, et al.
Publicado: (2016)

MethylExtract: High-Quality methylation maps and SNV calling from whole genome bisulfite sequencing data
por: Barturen, Guillermo, et al.
Publicado: (2014)

epiG: statistical inference and profiling of DNA methylation from whole-genome bisulfite sequencing data
por: Vincent, Martin, et al.
Publicado: (2017)

Statistically robust methylation calling for whole-transcriptome bisulfite sequencing reveals distinct methylation patterns for mouse RNAs
por: Legrand, Carine, et al.
Publicado: (2017)

Comparison and quantitative verification of mapping algorithms for whole-genome bisulfite sequencing
por: Kunde-Ramamoorthy, Govindarajan, et al.
Publicado: (2014)

Metheor: Ultrafast DNA methylation heterogeneity calculation from bisulfite read alignments
por: Lee, Dohoon, et al.
Publicado: (2023)

Whole-genome bisulfite sequencing with improved accuracy and cost
por: Suzuki, Masako, et al.
Publicado: (2018)

Amplification-free whole-genome bisulfite sequencing by post-bisulfite adaptor tagging
por: Miura, Fumihito, et al.
Publicado: (2012)

A mostly traditional approach improves alignment of bisulfite-converted DNA
por: Frith, Martin C., et al.
Publicado: (2012)

MethylScore, a pipeline for accurate and context-aware identification of differentially methylated regions from population-scale plant whole-genome bisulfite sequencing data
por: Hüther, Patrick, et al.
Publicado: (2022)

Objective and Comprehensive Evaluation of Bisulfite Short Read Mapping Tools
por: Tran, Hong, et al.
Publicado: (2014)

Bis-SNP: Combined DNA methylation and SNP calling for Bisulfite-seq data
por: Liu, Yaping, et al.
Publicado: (2012)

EpiDiverse Toolkit: a pipeline suite for the analysis of bisulfite sequencing data in ecological plant epigenetics
por: Nunn, Adam, et al.
Publicado: (2021)

Ultra-low-input, tagmentation-based whole-genome bisulfite sequencing
por: Adey, Andrew, et al.
Publicado: (2012)

Detection of differentially methylated regions from whole-genome bisulfite sequencing data without replicates
por: Wu, Hao, et al.
Publicado: (2015)

Quantification of DNA methylation independent of sodium bisulfite conversion using methylation‐sensitive restriction enzymes and digital PCR
por: Nell, Rogier J., et al.
Publicado: (2020)

RNA cytosine methylation analysis by bisulfite sequencing
por: Schaefer, Matthias, et al.
Publicado: (2009)

Gel-free multiplexed reduced representation bisulfite sequencing for large-scale DNA methylation profiling
por: Boyle, Patrick, et al.
Publicado: (2012)

Incorporating sequence quality data into alignment improves DNA read mapping
por: Frith, Martin C., et al.
Publicado: (2010)

Highly efficient single-stranded DNA ligation technique improves low-input whole-genome bisulfite sequencing by post-bisulfite adaptor tagging
por: Miura, Fumihito, et al.
Publicado: (2019)

A multi-split mapping algorithm for circular RNA, splicing, trans-splicing and fusion detection
por: Hoffmann, Steve, et al.
Publicado: (2014)

Investigating bisulfite short-read mapping failure with hairpin bisulfite sequencing data
por: Porter, Jacob, et al.
Publicado: (2015)

deepBlockAlign: a tool for aligning RNA-seq profiles of read block patterns
por: Langenberger, David, et al.
Publicado: (2012)

Bisulfite sequencing of chromatin immunoprecipitated DNA (BisChIP-seq) directly informs methylation status of histone-modified DNA
por: Statham, Aaron L., et al.
Publicado: (2012)

Fast and memory-efficient mapping of short bisulfite sequencing reads using a two-letter alphabet
por: de Sena Brandine, Guilherme, et al.
Publicado: (2021)

Sequential ChIP-bisulfite sequencing enables direct genome-scale investigation of chromatin and DNA methylation cross-talk
por: Brinkman, Arie B., et al.
Publicado: (2012)

In-solution hybrid capture of bisulfite-converted DNA for targeted bisulfite sequencing of 174 ADME genes
por: Ivanov, Maxim, et al.
Publicado: (2013)

Rapid quantification of DNA methylation through dNMP analysis following bisulfite-PCR
por: Yang, Inchul, et al.
Publicado: (2006)

The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote
por: Liao, Yang, et al.
Publicado: (2013)

Analyzing whole genome bisulfite sequencing data from highly divergent genotypes
por: Wulfridge, Phillip, et al.
Publicado: (2019)

Control of carry-over contamination for PCR-based DNA methylation quantification using bisulfite treated DNA
por: Tetzner, Reimo, et al.
Publicado: (2007)

A ligation assay for multiplex analysis of CpG methylation using bisulfite-treated DNA
por: Dahl, Christina, et al.
Publicado: (2007)

Laser capture microdissection–reduced representation bisulfite sequencing (LCM-RRBS) maps changes in DNA methylation associated with gonadectomy-induced adrenocortical neoplasia in the mouse
por: Schillebeeckx, Maximiliaan, et al.
Publicado: (2013)

Single-cell, locus-specific bisulfite sequencing (SLBS) for direct detection of epimutations in DNA methylation patterns
por: Gravina, Silvia, et al.
Publicado: (2015)

Cannot write session to /tmp/vufind_sessions/sess_mdpmm9ht9von38aq5i414s3bt4