Cargando…

Validation and assessment of variant calling pipelines for next-generation sequencing

BACKGROUND: The processing and analysis of the large scale data generated by next-generation sequencing (NGS) experiments is challenging and is a burgeoning area of new methods development. Several new bioinformatics tools have been developed for calling sequence variants from NGS data. Here, we val...

Descripción completa

Detalles Bibliográficos
Autores principales:	Pirooznia, Mehdi, Kramer, Melissa, Parla, Jennifer, Goes, Fernando S, Potash, James B, McCombie, W Richard, Zandi, Peter P
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	BioMed Central 2014
Materias:	Primary Research
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4129436/ https://www.ncbi.nlm.nih.gov/pubmed/25078893 http://dx.doi.org/10.1186/1479-7364-8-14

Ejemplares similares

A Hybrid Likelihood Model for Sequence-Based Disease Association Studies
por: Chen, Yun-Ching, et al.
Publicado: (2013)

Systematic review of genome-wide gene expression studies of bipolar disorder
por: Seifuddin, Fayaz, et al.
Publicado: (2013)

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

A comparative analysis of exome capture
por: Parla, Jennifer S, et al.
Publicado: (2011)

Whole-genome CNV analysis: advances in computational approaches
por: Pirooznia, Mehdi, et al.
Publicado: (2015)

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

Establishing the baseline level of repetitive element expression in the human cortex
por: Tyekucheva, Svitlana, et al.
Publicado: (2011)

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

Identification of cancer predisposition variants in apparently healthy individuals using a next-generation sequencing-based family genomics approach
por: Karageorgos, Ioannis, et al.
Publicado: (2015)

Toward a clinical diagnostic pipeline for SPINK1 intronic variants
por: Tang, Xin-Ying, et al.
Publicado: (2019)

Reproducibility of Variant Calls in Replicate Next Generation Sequencing Experiments
por: Qi, Yuan, et al.
Publicado: (2015)

SVAw - a web-based application tool for automated surrogate variable analysis of gene expression studies
por: Pirooznia, Mehdi, et al.
Publicado: (2013)

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

Affected Sib-Pair Analyses Identify Signaling Networks Associated With Social Behavioral Deficits in Autism
por: Pirooznia, Mehdi, et al.
Publicado: (2019)

A pipeline combining multiple strategies for prioritizing heterozygous variants for the identification of candidate genes in exome datasets
por: Requena, Teresa, et al.
Publicado: (2017)

Rapid detection of genetic mutations in individual breast cancer patients by next-generation DNA sequencing
por: Liu, Suqin, et al.
Publicado: (2015)

Targeted next generation sequencing identifies novel NOTCH3 gene mutations in CADASIL diagnostics patients
por: Maksemous, Neven, et al.
Publicado: (2016)

Prognostic factors of non-muscle invasive bladder cancer: a study based on next-generation sequencing
por: Shao, Yanxiang, et al.
Publicado: (2021)

Evaluating Variant Calling Tools for Non-Matched Next-Generation Sequencing Data
por: Sandmann, Sarah, et al.
Publicado: (2017)

Multiple Variant Calling Pipelines in Wheat Whole Exome Sequencing
por: Cagirici, H. Busra, et al.
Publicado: (2021)

Next-generation sequencing-based genetic landscape and its clinical implications for Chinese acute myeloid leukemia patients
por: Cao, Xin-xin, et al.
Publicado: (2018)

Improving bioinformatic pipelines for exome variant calling
por: Ji, Hanlee P
Publicado: (2012)

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)

Next-generation sequencing using a pre-designed gene panel for the molecular diagnosis of congenital disorders in pediatric patients
por: Lim, Eileen C. P., et al.
Publicado: (2015)

Base-calling for next-generation sequencing platforms
por: Ledergerber, Christian, et al.
Publicado: (2011)

Coval: Improving Alignment Quality and Variant Calling Accuracy for Next-Generation Sequencing Data
por: Kosugi, Shunichi, et al.
Publicado: (2013)

Next Generation House Call
por: Adams, Jamie L., et al.
Publicado: (2017)

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

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

An Outbreak of Anthrax
por: McCombie,
Publicado: (1915)

Correction: Coval: Improving Alignment Quality and Variant Calling Accuracy for Next-Generation Sequencing Data
por: Kosugi, Shunichi, et al.
Publicado: (2014)

A review of somatic single nucleotide variant calling algorithms for next-generation sequencing data
por: Xu, Chang
Publicado: (2018)

xAtlas: scalable small variant calling across heterogeneous next-generation sequencing experiments
por: Farek, Jesse, et al.
Publicado: (2023)

VDAP-GUI: a user-friendly pipeline for variant discovery and annotation of raw next-generation sequencing data
por: Menon, Ramesh, et al.
Publicado: (2016)

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

Modeling the next generation sequencing sample processing pipeline for the purposes of classification
por: Ghaffari, Noushin, 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)

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

HaploTypo: a variant-calling pipeline for phased genomes
por: Pegueroles, Cinta, et al.
Publicado: (2020)

Cannot write session to /tmp/vufind_sessions/sess_laig27d6vo1i4l4fu22ouhgb4c