Cargando…

ngs_backbone: a pipeline for read cleaning, mapping and SNP calling using Next Generation Sequence

BACKGROUND: The possibilities offered by next generation sequencing (NGS) platforms are revolutionizing biotechnological laboratories. Moreover, the combination of NGS sequencing and affordable high-throughput genotyping technologies is facilitating the rapid discovery and use of SNPs in non-model s...

Descripción completa

Detalles Bibliográficos
Autores principales:	Blanca, Jose M, Pascual, Laura, Ziarsolo, Peio, Nuez, Fernando, Cañizares, Joaquin
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	BioMed Central 2011
Materias:	Software
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3124440/ https://www.ncbi.nlm.nih.gov/pubmed/21635747 http://dx.doi.org/10.1186/1471-2164-12-285

Ejemplares similares

InteMAP: Integrated metagenomic assembly pipeline for NGS short reads
por: Lai, Binbin, et al.
Publicado: (2015)

K-seq, an affordable, reliable, and open Klenow NGS-based genotyping technology
por: Ziarsolo, Peio, et al.
Publicado: (2021)

FastProNGS: fast preprocessing of next-generation sequencing reads
por: Liu, Xiaoshuang, et al.
Publicado: (2019)

SNP-PHAGE – High throughput SNP discovery pipeline
por: Matukumalli, Lakshmi K, et al.
Publicado: (2006)

NEAT: a framework for building fully automated NGS pipelines and analyses
por: Schorderet, Patrick
Publicado: (2016)

SEQprocess: a modularized and customizable pipeline framework for NGS processing in R package
por: Joo, Taewoon, et al.
Publicado: (2019)

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

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

Variation Revealed by SNP Genotyping and Morphology Provides Insight into the Origin of the Tomato
por: Blanca, Jose, et al.
Publicado: (2012)

Vipie: web pipeline for parallel characterization of viral populations from multiple NGS samples
por: Lin, Jake, et al.
Publicado: (2017)

ClinQC: a tool for quality control and cleaning of Sanger and NGS data in clinical research
por: Pandey, Ram Vinay, et al.
Publicado: (2016)

Teaser: Individualized benchmarking and optimization of read mapping results for NGS data
por: Smolka, Moritz, et al.
Publicado: (2015)

TreeToReads - a pipeline for simulating raw reads from phylogenies
por: McTavish, Emily Jane, et al.
Publicado: (2017)

Transcriptome characterization and high throughput SSRs and SNPs discovery in Cucurbita pepo (Cucurbitaceae)
por: Blanca, José, et al.
Publicado: (2011)

Ioncopy: an R Shiny app to call copy number alterations in targeted NGS data
por: Budczies, Jan, et al.
Publicado: (2018)

ImmunoDataAnalyzer: a bioinformatics pipeline for processing barcoded and UMI tagged immunological NGS data
por: Vetter, Julia, et al.
Publicado: (2022)

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

ExUTR: a novel pipeline for large-scale prediction of 3′-UTR sequences from NGS data
por: Huang, Zixia, et al.
Publicado: (2017)

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

ToTem: a tool for variant calling pipeline optimization
por: Tom, Nikola, et al.
Publicado: (2018)

Gencore: an efficient tool to generate consensus reads for error suppressing and duplicate removing of NGS data
por: Chen, Shifu, et al.
Publicado: (2019)

SNPhylo: a pipeline to construct a phylogenetic tree from huge SNP data
por: Lee, Tae-Ho, et al.
Publicado: (2014)

Quantitative genetic analysis of floral traits shows current limits but potential evolution in the wild
por: Castellanos, Maria Clara, et al.
Publicado: (2023)

NGS-Logistics: federated analysis of NGS sequence variants across multiple locations
por: Ardeshirdavani, Amin, et al.
Publicado: (2014)

Duet: SNP-assisted structural variant calling and phasing using Oxford nanopore sequencing
por: Zhou, Yekai, et al.
Publicado: (2022)

Comparison of SNP Calling Pipelines and NGS Platforms to Predict the Genomic Regions Harboring Candidate Genes for Nodulation in Cultivated Peanut
por: Peng, Ze, et al.
Publicado: (2020)

SVNN: an efficient PacBio-specific pipeline for structural variations calling using neural networks
por: Akbarinejad, Shaya, et al.
Publicado: (2021)

4Pipe4 – A 454 data analysis pipeline for SNP detection in datasets with no reference sequence or strain information
por: Pina-Martins, Francisco, et al.
Publicado: (2016)

BreakAlign: a Perl program to align chimaeric (split) genomic NGS reads and allow visual confirmation of novel retroviral integrations
por: Marchi, Emanuele, et al.
Publicado: (2022)

FiNGS: high quality somatic mutations using filters for next generation sequencing
por: Wardell, Christopher Paul, et al.
Publicado: (2021)

NGS-Integrator: An efficient tool for combining multiple NGS data tracks using minimum Bayes’ factors
por: Wen, Bronte, et al.
Publicado: (2020)

CLOTU: An online pipeline for processing and clustering of 454 amplicon reads into OTUs followed by taxonomic annotation
por: Kumar, Surendra, et al.
Publicado: (2011)

SeqTrim: a high-throughput pipeline for pre-processing any type of sequence read
por: Falgueras, Juan, et al.
Publicado: (2010)

TOGGLE: toolbox for generic NGS analyses
por: Monat, Cécile, et al.
Publicado: (2015)

QualitySNP: a pipeline for detecting single nucleotide polymorphisms and insertions/deletions in EST data from diploid and polyploid species
por: Tang, Jifeng, et al.
Publicado: (2006)

ngs.plot: Quick mining and visualization of next-generation sequencing data by integrating genomic databases
por: Shen, Li, et al.
Publicado: (2014)

QuickNGS elevates Next-Generation Sequencing data analysis to a new level of automation
por: Wagle, Prerana, et al.
Publicado: (2015)

Fast-GBS: a new pipeline for the efficient and highly accurate calling of SNPs from genotyping-by-sequencing data
por: Torkamaneh, Davoud, et al.
Publicado: (2017)

SNPAAMapperT2K: A genome-wide SNP downstream analysis and annotation pipeline for species annotated with NCBI.tbl data files
por: Bai, Yongsheng
Publicado: (2014)

KvarQ: targeted and direct variant calling from fastq reads of bacterial genomes
por: Steiner, Andreas, et al.
Publicado: (2014)

Cannot write session to /tmp/vufind_sessions/sess_1gr5toiti7eoisjhehk22qsevi