Systematic evaluation of error rates and causes in short samples in next-generation sequencing

Systematic evaluation of cell-SELEX enriched aptamers binding to breast cancer cells

(2018) Laia Civit et al.   BIOCHIMIE

PhredEM: a phred-score-informed genotype-calling approach for next-generation sequencing studies

(2017) Peizhou Liao et al.   GENETIC EPIDEMIOLOGY

An adaptive decorrelation method removes Illumina DNA base-calling errors caused by crosstalk between adjacent clusters

(2017) Bo Wang et al.   Scientific Reports

Click Reaction on Solid Phase Enables High Fidelity Synthesis of Nucleobase-Modified DNA

(2016) Fabian Tolle et al.   BIOCONJUGATE CHEMISTRY

Reproducibility of Illumina platform deep sequencing errors allows accurate determination of DNA barcodes in cells

(2016) Joost B. Beltman et al.   BMC BIOINFORMATICS

A benchmark study on error-correction by read-pairing and tag-clustering in amplicon-based deep sequencing

(2016) Tian-Hao Zhang et al.   BMC GENOMICS

AptaPLEX – A dedicated, multithreaded demultiplexer for HT-SELEX data

(2016) Jan Hoinka et al.   METHODS

Analyzing HT-SELEX data with the Galaxy Project tools – A web based bioinformatics platform for biomedical research

(2016) William H. Thiel et al.   METHODS

A Versatile Approach Towards Nucleobase-Modified Aptamers

(2015) Fabian Tolle et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

APTANI: a computational tool to select aptamers through sequence-structure motif analysis of HT-SELEX data

(2015) J. Caroli et al.   BIOINFORMATICS

Primer ID Validates Template Sampling Depth and Greatly Reduces the Error Rate of Next-Generation Sequencing of HIV-1 Genomic RNA Populations

(2015) Shuntai Zhou et al.   JOURNAL OF VIROLOGY

Insight into biases and sequencing errors for amplicon sequencing with the Illumina MiSeq platform

(2015) Melanie Schirmer et al.   NUCLEIC ACIDS RESEARCH

NGS-eval: NGS Error analysis and novel sequence VAriant detection tooL

(2015) Ali May et al.   NUCLEIC ACIDS RESEARCH

Aptamer Selection Technology and Recent Advances

(2015) Michael Blind et al.   Molecular Therapy-Nucleic Acids

Selection of a DNA aptamer against norovirus capsid protein VP1

(2013) Rico Beier et al.   FEMS MICROBIOLOGY LETTERS

Ethynyl Side Chain Hydration during Synthesis and Workup of “Clickable” Oligonucleotides: Bypassing Acetyl Group Formation by Triisopropylsilyl Protection

(2013) Sachin A. Ingale et al.   JOURNAL OF ORGANIC CHEMISTRY

QPLOT: A Quality Assessment Tool for Next Generation Sequencing Data

(2013) Bingshan Li et al.   Biomed Research International

Optimizing illumina next-generation sequencing library preparation for extremely at-biased genomes

(2012) Samuel O Oyola et al.   BMC GENOMICS

Quake: quality-aware detection and correction of sequencing errors

(2012) David R Kelley et al.   GENOME BIOLOGY

All your base: a fast and accurate probabilistic approach to base calling

(2012) Tim Massingham et al.   GENOME BIOLOGY

Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform

(2011) Martin Kircher et al.   NUCLEIC ACIDS RESEARCH

Nucleotide Bias Observed with a Short SELEX RNA Aptamer Library

(2011) William H. Thiel et al.   Nucleic Acid Therapeutics

Monitoring Genomic Sequences during SELEX Using High-Throughput Sequencing: Neutral SELEX

(2010) Bob Zimmermann et al.   PLoS One

BayesCall: A model-based base-calling algorithm for high-throughput short-read sequencing

(2009) W.-C. Kao et al.   GENOME RESEARCH

The challenges of sequencing by synthesis

(2009) Carl W Fuller et al.   NATURE BIOTECHNOLOGY

Improved base calling for the Illumina Genome Analyzer using machine learning strategies

(2009) Martin Kircher et al.   GENOME BIOLOGY

Substantial biases in ultra-short read data sets from high-throughput DNA sequencing

(2008) J. C. Dohm et al.   NUCLEIC ACIDS RESEARCH