Cargando…

CAPRG: Sequence Assembling Pipeline for Next Generation Sequencing of Non-Model Organisms

Our goal is to introduce and describe the utility of a new pipeline “Contigs Assembly Pipeline using Reference Genome” (CAPRG), which has been developed to assemble “long sequence reads” for non-model organisms by leveraging a reference genome of a closely related phylogenetic relative. To facilitat...

Descripción completa

Detalles Bibliográficos
Autores principales:	Rawat, Arun, Elasri, Mohamed O., Gust, Kurt A., George, Glover, Pham, Don, Scanlan, Leona D., Vulpe, Chris, Perkins, Edward J.
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Public Library of Science 2012
Materias:	Research Article
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3272009/ https://www.ncbi.nlm.nih.gov/pubmed/22319566 http://dx.doi.org/10.1371/journal.pone.0030370

Ejemplares similares

Quail Genomics: a knowledgebase for Northern bobwhite
por: Rawat, Arun, et al.
Publicado: (2010)

Multiple environmental stressors induce complex transcriptomic responses indicative of phenotypic outcomes in Western fence lizard
por: Gust, Kurt A., et al.
Publicado: (2018)

Modeling the next generation sequencing sample processing pipeline for the purposes of classification
por: Ghaffari, Noushin, et al.
Publicado: (2013)

An integrated pipeline for next-generation sequencing and annotation of mitochondrial genomes
por: Jex, Aaron R., et al.
Publicado: (2010)

Validation and assessment of variant calling pipelines for next-generation sequencing
por: Pirooznia, Mehdi, et al.
Publicado: (2014)

From Sequencer to Supercomputer: An Automatic Pipeline for Managing and Processing Next Generation Sequencing Data
por: Camerlengo, Terry, et al.
Publicado: (2012)

Microsatellites for Next-Generation Ecologists: A Post-Sequencing Bioinformatics Pipeline
por: Fernandez-Silva, Iria, et al.
Publicado: (2013)

Integrating Functional Analysis in the Next-Generation Sequencing Diagnostic Pipeline of RASopathies
por: Leung, Gordon K. C., et al.
Publicado: (2018)

Generation of Artificial FASTQ Files to Evaluate the Performance of Next-Generation Sequencing Pipelines
por: Frampton, Matthew, et al.
Publicado: (2012)

Tablet—next generation sequence assembly visualization
por: Milne, Iain, et al.
Publicado: (2010)

An Integrated SNP Mining and Utilization (ISMU) Pipeline for Next Generation Sequencing Data
por: Azam, Sarwar, et al.
Publicado: (2014)

Next Generation Sequence Analysis and Computational Genomics Using Graphical Pipeline Workflows
por: Torri, Federica, et al.
Publicado: (2012)

Comparison of seven SNP calling pipelines for the next-generation sequencing data of chickens
por: Liu, Jing, et al.
Publicado: (2022)

A Pipeline for the Development of Microsatellite Markers using Next Generation Sequencing Data
por: Antunes, Adriana Maria, et al.
Publicado: (2022)

Performance comparison of next generation sequencing analysis pipelines for HIV-1 drug resistance testing
por: Lee, Emma R., et al.
Publicado: (2020)

Launching genomics into the cloud: deployment of Mercury, a next generation sequence analysis pipeline
por: Reid, Jeffrey G, et al.
Publicado: (2014)

ViennaNGS: A toolbox for building efficient next- generation sequencing analysis pipelines
por: Wolfinger, Michael T., et al.
Publicado: (2015)

Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease
por: Dilliott, Allison A., et al.
Publicado: (2018)

Systematic comparison of germline variant calling pipelines cross multiple next-generation sequencers
por: Chen, Jiayun, et al.
Publicado: (2019)

MAECI: A pipeline for generating consensus sequence with nanopore sequencing long-read assembly and error correction
por: Lang, Jidong
Publicado: (2022)

DDBJ Read Annotation Pipeline: A Cloud Computing-Based Pipeline for High-Throughput Analysis of Next-Generation Sequencing Data
por: Nagasaki, Hideki, et al.
Publicado: (2013)

SNPAAMapper: An efficient genome-wide SNP variant analysis pipeline for next-generation sequencing data
por: Bai, Yongsheng, et al.
Publicado: (2013)

Reliability of genomic variants across different next-generation sequencing platforms and bioinformatic processing pipelines
por: Weißbach, Stephan, et al.
Publicado: (2021)

GAM-NGS: genomic assemblies merger for next generation sequencing
por: Vicedomini, Riccardo, et al.
Publicado: (2013)

SeedsGraph: an efficient assembler for next-generation sequencing data
por: Wang, Chunyu, et al.
Publicado: (2015)

ECuADOR—Easy Curation of Angiosperm Duplicated Organellar Regions, a tool for cleaning and curating plastomes assembled from next generation sequencing pipelines
por: Armijos Carrion, Angelo D., et al.
Publicado: (2020)

ngs_backbone: a pipeline for read cleaning, mapping and SNP calling using Next Generation Sequence
por: Blanca, Jose M, et al.
Publicado: (2011)

A fully automated pipeline for quantitative genotype calling from next generation sequencing data in autopolyploids
por: Pereira, Guilherme S., et al.
Publicado: (2018)

ANASTASIA: An Automated Metagenomic Analysis Pipeline for Novel Enzyme Discovery Exploiting Next Generation Sequencing Data
por: Koutsandreas, Theodoros, et al.
Publicado: (2019)

MIRACUM-Pipe: An Adaptable Pipeline for Next-Generation Sequencing Analysis, Reporting, and Visualization for Clinical Decision Making
por: Metzger, Patrick, et al.
Publicado: (2023)

The Listeria monocytogenes Core-Genome Sequence Typer (LmCGST): a bioinformatic pipeline for molecular characterization with next-generation sequence data
por: Pightling, Arthur W., et al.
Publicado: (2015)

Assessment of Metagenomic Assembly Using Simulated Next Generation Sequencing Data
por: Mende, Daniel R., et al.
Publicado: (2012)

Assembly of non-unique insertion content using next-generation sequencing
por: Parrish, Nathaniel, et al.
Publicado: (2011)

Review of General Algorithmic Features for Genome Assemblers for Next Generation Sequencers
por: Wajid, Bilal, et al.
Publicado: (2012)

Virome assembly and annotation in brain tissue based on next‐generation sequencing
por: Yuan, Zihao, et al.
Publicado: (2020)

Adaptive bandwidth kernel density estimation for next-generation sequencing data
por: Ramachandran, Parameswaran, et al.
Publicado: (2013)

Next-Generation Sequencing
por: Xiong, Momiao, et al.
Publicado: (2010)

Next-generation sequencing
por: Reis-Filho, Jorge S
Publicado: (2009)

VPipe: an Automated Bioinformatics Platform for Assembly and Management of Viral Next-Generation Sequencing Data
por: Wagner, Darlene D., et al.
Publicado: (2022)

A cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples
por: Naccache, Samia N., et al.
Publicado: (2014)

Cannot write session to /tmp/vufind_sessions/sess_romjaj5dsnq4bl69lch02dvolm