Cargando…

High-performance pipeline for MutMap and QTL-seq

SUMMARY: Bulked segregant analysis implemented in MutMap and QTL-seq is a powerful and efficient method to identify loci contributing to important phenotypic traits. However, the previous pipelines were not user-friendly to install and run. Here, we describe new pipelines for MutMap and QTL-seq. The...

Descripción completa

Detalles Bibliográficos
Autores principales:	Sugihara, Yu, Young, Lester, Yaegashi, Hiroki, Natsume, Satoshi, Shea, Daniel J., Takagi, Hiroki, Booker, Helen, Innan, Hideki, Terauchi, Ryohei, Abe, Akira
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	PeerJ Inc. 2022
Materias:	Bioinformatics
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8935991/ https://www.ncbi.nlm.nih.gov/pubmed/35321412 http://dx.doi.org/10.7717/peerj.13170

Ejemplares similares

MutMap+: Genetic Mapping and Mutant Identification without Crossing in Rice
por: Fekih, Rym, et al.
Publicado: (2013)

QTL-seq analysis identifies two genomic regions determining the heading date of foxtail millet, Setaria italica (L.) P.Beauv.
por: Yoshitsu, Yuki, et al.
Publicado: (2017)

The Power of QTL Mapping with RILs
por: Takuno, Shohei, et al.
Publicado: (2012)

QTL Map Meets Population Genomics: An Application to Rice
por: Fawcett, Jeffrey A., et al.
Publicado: (2013)

Exome QTL-seq maps monogenic locus and QTLs in barley
por: Hisano, Hiroshi, et al.
Publicado: (2017)

Fine Mapping of Stripe-Rust-Resistance Gene YrJ22 in Common Wheat by BSR-Seq and MutMap-Based Sequencing
por: Chen, Can, et al.
Publicado: (2022)

WB1, a Regulator of Endosperm Development in Rice, Is Identified by a Modified MutMap Method
por: Wang, Hong, et al.
Publicado: (2018)

Gene identification and transcriptome analysis of low cadmium accumulation rice mutant (lcd1) in response to cadmium stress using MutMap and RNA-seq
por: Cao, Zhen Zhen, et al.
Publicado: (2019)

Mutation incidence and coincidence in non small-cell lung cancer: meta-analyses by ethnicity and histology (mutMap)
por: Dearden, S., et al.
Publicado: (2013)

Genome Analysis Revives a Forgotten Hybrid Crop Edo-dokoro in the Genus Dioscorea
por: Natsume, Satoshi, et al.
Publicado: (2022)

Unipro UGENE NGS pipelines and components for variant calling, RNA-seq and ChIP-seq data analyses
por: Golosova, Olga, et al.
Publicado: (2014)

Software pipelines for RNA-Seq, ChIP-Seq and germline variant calling analyses in common workflow language (CWL)
por: Kyritsis, Konstantinos A., et al.
Publicado: (2023)

I-ATAC: interactive pipeline for the management and pre-processing of ATAC-seq samples
por: Ahmed, Zeeshan, et al.
Publicado: (2017)

Genome analysis of the foxtail millet pathogen Sclerospora graminicola reveals the complex effector repertoire of graminicolous downy mildews
por: Kobayashi, Michie, et al.
Publicado: (2017)

Genome analyses reveal the hybrid origin of the staple crop white Guinea yam (Dioscorea rotundata)
por: Sugihara, Yu, et al.
Publicado: (2020)

MutMap Approach Enables Rapid Identification of Candidate Genes and Development of Markers Associated With Early Flowering and Enhanced Seed Size in Chickpea (Cicer arietinum L.)
por: Manchikatla, Praveen Kumar, et al.
Publicado: (2021)

MutRank: an R shiny web-application for exploratory targeted mutual rank-based coexpression analyses integrated with user-provided supporting information
por: Poretsky, Elly, et al.
Publicado: (2020)

The impact of Docker containers on the performance of genomic pipelines
por: Di Tommaso, Paolo, et al.
Publicado: (2015)

Compi: a framework for portable and reproducible pipelines
por: López-Fernández, Hugo, et al.
Publicado: (2021)

Funmap2: an R package for QTL mapping using longitudinal phenotypes
por: Wang, Nating, et al.
Publicado: (2019)

DRUID: a pipeline for transcriptome-wide measurements of mRNA stability
por: Lugowski, Andrew, et al.
Publicado: (2018)

Benchmark datasets for phylogenomic pipeline validation, applications for foodborne pathogen surveillance
por: Timme, Ruth E., et al.
Publicado: (2017)

A supertree pipeline for summarizing phylogenetic and taxonomic information for millions of species
por: Redelings, Benjamin D., et al.
Publicado: (2017)

BingleSeq: a user-friendly R package for bulk and single-cell RNA-Seq data analysis
por: Dimitrov, Daniel, et al.
Publicado: (2020)

The Bacteria Genome Pipeline (BAGEP): an automated, scalable workflow for bacteria genomes with Snakemake
por: Olawoye, Idowu B., et al.
Publicado: (2020)

An Image Analysis Pipeline for Quantifying the Features of Fluorescently-Labeled Biomolecular Condensates in Cells
por: Baggett, David W., et al.
Publicado: (2022)

Snaq: A Dynamic Snakemake Pipeline for Microbiome Data Analysis With QIIME2
por: Mohsen, Attayeb, et al.
Publicado: (2022)

Real-time pneumonia prediction using pipelined spark and high-performance computing
por: Ravikumar, Aswathy, et al.
Publicado: (2023)

Mapping-by-Sequencing via MutMap Identifies a Mutation in ZmCLE7 Underlying Fasciation in a Newly Developed EMS Mutant Population in an Elite Tropical Maize Inbred
por: Tran, Quan Hong, et al.
Publicado: (2020)

QTL‐seq for rapid identification of candidate genes for 100‐seed weight and root/total plant dry weight ratio under rainfed conditions in chickpea
por: Singh, Vikas K., et al.
Publicado: (2016)

The classification of EEG-based winking signals: a transfer learning and random forest pipeline
por: Mahendra Kumar, Jothi Letchumy, et al.
Publicado: (2021)

Tailer: a pipeline for sequencing-based analysis of nonpolyadenylated RNA 3′ end processing
por: Nicholson-Shaw, Tim, et al.
Publicado: (2022)

Robustness analysis of metabolic predictions in algal microbial communities based on different annotation pipelines
por: Karimi, Elham, et al.
Publicado: (2021)

MIntO: A Modular and Scalable Pipeline For Microbiome Metagenomic and Metatranscriptomic Data Integration
por: Saenz, Carmen, et al.
Publicado: (2022)

Integrated mRNA-seq and miRNA-seq analysis of goat fibroblasts response to Brucella Melitensis strain M5-90
por: Li, Baobao, et al.
Publicado: (2021)

3′ RNA-seq is superior to standard RNA-seq in cases of sparse data but inferior at identifying toxicity pathways in a model organism
por: McClure, Ryan S., et al.
Publicado: (2023)

Getting the most out of RNA-seq data analysis
por: Khang, Tsung Fei, et al.
Publicado: (2015)

FastViromeExplorer: a pipeline for virus and phage identification and abundance profiling in metagenomics data
por: Tithi, Saima Sultana, et al.
Publicado: (2018)

GenoDup Pipeline: a tool to detect genome duplication using the dS-based method
por: Mao, Yafei
Publicado: (2019)

Bioinformatic pipelines for whole transcriptome sequencing data exploitation in leukemia patients with complex structural variants
por: Hynst, Jakub, et al.
Publicado: (2019)

Cannot write session to /tmp/vufind_sessions/sess_g32d5ccf3nh31lvsb080lkkf94