Cargando…

Synthetic Spike-in Standards Improve Run-Specific Systematic Error Analysis for DNA and RNA Sequencing

While the importance of random sequencing errors decreases at higher DNA or RNA sequencing depths, systematic sequencing errors (SSEs) dominate at high sequencing depths and can be difficult to distinguish from biological variants. These SSEs can cause base quality scores to underestimate the probab...

Descripción completa

Detalles Bibliográficos
Autores principales:	Zook, Justin M., Samarov, Daniel, McDaniel, Jennifer, Sen, Shurjo K., Salit, Marc
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/PMC3409179/ https://www.ncbi.nlm.nih.gov/pubmed/22859977 http://dx.doi.org/10.1371/journal.pone.0041356

Ejemplares similares

PEPR: pipelines for evaluating prokaryotic references
por: Olson, Nathan D., et al.
Publicado: (2016)

Genomes in a bottle: creating standard reference materials for genomic variation - why, what and how?
por: Zook, Justin M, et al.
Publicado: (2011)

Genome-wide reconstruction of complex structural variants using read clouds
por: Spies, Noah, et al.
Publicado: (2017)

Using mixtures of biological samples as process controls for RNA-sequencing experiments
por: Parsons, Jerod, et al.
Publicado: (2015)

Synthetic spike-in standards for high-throughput 16S rRNA gene amplicon sequencing
por: Tourlousse, Dieter M., et al.
Publicado: (2017)

Medical implications of technical accuracy in genome sequencing
por: Goldfeder, Rachel L., et al.
Publicado: (2016)

synDNA—a Synthetic DNA Spike-in Method for Absolute Quantification of Shotgun Metagenomic Sequencing
por: Zaramela, Livia S., et al.
Publicado: (2022)

External RNA Controls Consortium Beta Version Update
por: Lee, Hangnoh, et al.
Publicado: (2016)

MESA: automated assessment of synthetic DNA fragments and simulation of DNA synthesis, storage, sequencing and PCR errors
por: Schwarz, Michael, et al.
Publicado: (2020)

An open resource for accurately benchmarking small variant and reference calls
por: Zook, Justin M., et al.
Publicado: (2019)

Correcting errors in synthetic DNA through consensus shuffling
por: Binkowski, Brock F., et al.
Publicado: (2005)

Development and Characterization of Reference Materials for Genetic Testing: Focus on Public Partnerships
por: Kalman, Lisa V., et al.
Publicado: (2016)

Open-access synthetic spike-in mRNA-seq data for cancer gene fusions
por: Tembe, Waibhav D, et al.
Publicado: (2014)

Repair-Mediated Duplication by Capture of Proximal Chromosomal DNA Has Shaped Vertebrate Genome Evolution
por: Pace, John K., et al.
Publicado: (2009)

A Rigorous Interlaboratory Examination of the Need to Confirm Next-Generation Sequencing–Detected Variants with an Orthogonal Method in Clinical Genetic Testing
por: Lincoln, Stephen E., et al.
Publicado: (2019)

High-coverage, long-read sequencing of Han Chinese trio reference samples
por: Wang, Ying-Chih, et al.
Publicado: (2019)

Sensitive and reproducible cell-free methylome quantification with synthetic spike-in controls
por: Wilson, Samantha L., et al.
Publicado: (2022)

Inferring Demography from Runs of Homozygosity in Whole-Genome Sequence, with Correction for Sequence Errors
por: MacLeod, Iona M., et al.
Publicado: (2013)

A Standard Error: Distinguishing Standard Deviation From Standard Error
por: Carter, Rickey E.
Publicado: (2013)

July Spike in Fatal Medication Errors
por: Phillips, David P., et al.
Publicado: (2010)

Specifications of Standards in Systems and Synthetic Biology
por: Schreiber, Falk, et al.
Publicado: (2015)

Synthetic Standards Combined With Error and Bias Correction Improve the Accuracy and Quantitative Resolution of Antibody Repertoire Sequencing in Human Naïve and Memory B Cells
por: Friedensohn, Simon, et al.
Publicado: (2018)

Standard deviation and standard error of the mean
por: Lee, Dong Kyu, et al.
Publicado: (2015)

Sequence verification of synthetic DNA by assembly of sequencing reads
por: Wilson, Mandy L., et al.
Publicado: (2013)

A minimum information standard for reproducing bench-scale bacterial cell growth and productivity
por: Hecht, Ariel, et al.
Publicado: (2018)

Assembly and annotation of an Ashkenazi human reference genome
por: Shumate, Alaina, et al.
Publicado: (2020)

Comparison of DNA Extracted from Pediatric Saliva, Gingival Crevicular Fluid and Site-Specific Biofilm Samples
por: Emett, Jason, et al.
Publicado: (2020)

Ancient DNA sequence revealed by error-correcting codes
por: Brandão, Marcelo M., et al.
Publicado: (2015)

Mapping DNA polymerase errors by single-molecule sequencing
por: Lee, David F., et al.
Publicado: (2016)

Levenshtein error-correcting barcodes for multiplexed DNA sequencing
por: Buschmann, Tilo, et al.
Publicado: (2013)

Quantification of synthetic errors during chemical synthesis of DNA and its suppression by non-canonical nucleosides
por: Masaki, Yoshiaki, et al.
Publicado: (2022)

Sequence-specific error profile of Illumina sequencers
por: Nakamura, Kensuke, et al.
Publicado: (2011)

svclassify: a method to establish benchmark structural variant calls
por: Parikh, Hemang, et al.
Publicado: (2016)

Non-biological synthetic spike-in controls and the AMPtk software pipeline improve mycobiome data
por: Palmer, Jonathan M., et al.
Publicado: (2018)

Bioreactor virome metagenomics sequencing using DNA spike-ins
por: Cremers, Geert, et al.
Publicado: (2018)

Synthetic Sequencing Standards: A Guide to Database Choice for Rumen Microbiota Amplicon Sequencing Analysis
por: Smith, Paul E., et al.
Publicado: (2020)

Interrupted coding sequences in Mycobacterium smegmatis: authentic mutations or sequencing errors?
por: Deshayes, Caroline, et al.
Publicado: (2007)

Endonuclease-independent insertion provides an alternative pathway for L1 retrotransposition in the human genome
por: Sen, Shurjo K., et al.
Publicado: (2007)

Synthetic microbe communities provide internal reference standards for metagenome sequencing and analysis
por: Hardwick, Simon A., et al.
Publicado: (2018)

Data explosion during COVID-19: A call for collaboration with the tech industry & data scrutiny
por: Hechenbleikner, Elizabeth M., et al.
Publicado: (2020)

Cannot write session to /tmp/vufind_sessions/sess_skffiei0s1imjm8isonnlicbjg