Cargando…

UrQt: an efficient software for the Unsupervised Quality trimming of NGS data

BACKGROUND: Quality control is a necessary step of any Next Generation Sequencing analysis. Although customary, this step still requires manual interventions to empirically choose tuning parameters according to various quality statistics. Moreover, current quality control procedures that provide a “...

Descripción completa

Detalles Bibliográficos
Autores principales:	Modolo, Laurent, Lerat, Emmanuelle
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	BioMed Central 2015
Materias:	Software
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4450468/ https://www.ncbi.nlm.nih.gov/pubmed/25924884 http://dx.doi.org/10.1186/s12859-015-0546-8

Ejemplares similares

SeqPurge: highly-sensitive adapter trimming for paired-end NGS data
por: Sturm, Marc, et al.
Publicado: (2016)

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

AMLVaran: a software approach to implement variant analysis of targeted NGS sequencing data in an oncological care setting
por: Wünsch, Christian, et al.
Publicado: (2020)

DCE@urLAB: a dynamic contrast-enhanced MRI pharmacokinetic analysis tool for preclinical data
por: Ortuño, Juan E, et al.
Publicado: (2013)

pTrimmer: An efficient tool to trim primers of multiplex deep sequencing data
por: Zhang, Xiaolong, et al.
Publicado: (2019)

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

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

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

Conbase: a software for unsupervised discovery of clonal somatic mutations in single cells through read phasing
por: Hård, Joanna, et al.
Publicado: (2019)

ImmunExplorer (IMEX): a software framework for diversity and clonality analyses of immunoglobulins and T cell receptors on the basis of IMGT/HighV-QUEST preprocessed NGS data
por: Schaller, Susanne, et al.
Publicado: (2015)

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

SeQual-Stream: approaching stream processing to quality control of NGS datasets
por: Castellanos-Rodríguez, Óscar, et al.
Publicado: (2023)

“One code to find them all”: a perl tool to conveniently parse RepeatMasker output files
por: Bailly-Bechet, Marc, et al.
Publicado: (2014)

SUSHI: an exquisite recipe for fully documented, reproducible and reusable NGS data analysis
por: Hatakeyama, Masaomi, et al.
Publicado: (2016)

MegaPath: sensitive and rapid pathogen detection using metagenomic NGS data
por: Leung, Chi-Ming, et al.
Publicado: (2020)

ggcoverage: an R package to visualize and annotate genome coverage for various NGS data
por: Song, Yabing, et al.
Publicado: (2023)

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

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

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

SummonChimera infers integrated viral genomes with nucleotide precision from NGS data
por: Katz, Joshua P, et al.
Publicado: (2014)

Cnidaria: fast, reference-free clustering of raw and assembled genome and transcriptome NGS data
por: Aflitos, Saulo Alves, et al.
Publicado: (2015)

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

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)

GASAL2: a GPU accelerated sequence alignment library for high-throughput NGS data
por: Ahmed, Nauman, et al.
Publicado: (2019)

ITSxpress: Software to rapidly trim internally transcribed spacer sequences with quality scores for marker gene analysis
por: Rivers, Adam R., et al.
Publicado: (2018)

FastqCleaner: an interactive Bioconductor application for quality-control, filtering and trimming of FASTQ files
por: Roser, Leandro Gabriel, et al.
Publicado: (2019)

CHANCE: comprehensive software for quality control and validation of ChIP-seq data
por: Diaz, Aaron, et al.
Publicado: (2012)

ADEPT, a dynamic next generation sequencing data error-detection program with trimming
por: Feng, Shihai, et al.
Publicado: (2016)

QCScreen: a software tool for data quality control in LC-HRMS based metabolomics
por: Simader, Alexandra Maria, et al.
Publicado: (2015)

CAPL: an efficient association software package using family and case-control data and accounting for population stratification
por: Chung, Ren-Hua, et al.
Publicado: (2011)

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

Simplifier: a web tool to eliminate redundant NGS contigs
por: Ramos, Rommel Thiago Jucá, et al.
Publicado: (2012)

systemPipeR: NGS workflow and report generation environment
por: H. Backman, Tyler W., et al.
Publicado: (2016)

The Gaggle: An open-source software system for integrating bioinformatics software and data sources
por: Shannon, Paul T, et al.
Publicado: (2006)

DiviK: divisive intelligent K-means for hands-free unsupervised clustering in big biological data
por: Mrukwa, Grzegorz, et al.
Publicado: (2022)

A New Genome-Wide Method to Track Horizontally Transferred Sequences: Application to Drosophila
por: Modolo, Laurent, et al.
Publicado: (2014)

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

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

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

Cannot write session to /tmp/vufind_sessions/sess_vfbp56rc1o5tdhnk1hg43fi7kd