Results 1 to 10 of about 375,647 (115)
Trimmomatic: a flexible trimmer for Illumina sequence data. [PDF]
Bioinformatics, 2014 Abstract Motivation: Although many next-generation sequencing (NGS) read preprocessing tools already existed, we could not find any tool or combination of tools that met our requirements in terms of flexibility, correct handling of paired-end data and high performance.
Björn Usadel
exaly +8 more sources
Sequence-specific error profile of Illumina sequencers. [PDF]
Nucleic Acids Research, 2011 We identified the sequence-specific starting positions of consecutive miscalls in the mapping of reads obtained from the Illumina Genome Analyser (GA). Detailed analysis of the miscall pattern indicated that the underlying mechanism involves sequence-specific interference of the base elongation process during sequencing. The two major sequence patterns
Hiroki Takahashi +2 more
exaly +3 more sources
Improved Protocols for Illumina Sequencing [PDF]
Current Protocols in Human Genetics, 2013 AbstractIn this unit, we describe a set of improvements that have been made to the standard Illumina protocols to make the sequencing process more reliable in a high‐throughput environment, reduce amplification bias, narrow the distribution of insert sizes, and reliably obtain high yields of data. Curr. Protoc. Hum. Genet. 79:18.2.1‐18.2.42.
Iraad F, Bronner +3 more
+6 more sources
Sequencing error profiles of Illumina sequencing instruments [PDF]
NAR Genomics and Bioinformatics, 2021 Abstract Sequencing technology has achieved great advances in the past decade. Studies have previously shown the quality of specific instruments in controlled conditions. Here, we developed a method able to retroactively determine the error rate of most public sequencing datasets.
Nicholas Stoler, Anton Nekrutenko
openaire +2 more sources
Review on Illumina Sequencing Technology
Austin Journal of Veterinary Science & Animal Husbandry, 2022 Illumina sequencing process utilizes biochemical methods to determine the correct order of nucleotide bases in a deoxyribonucleic acid. Macromolecule using sequencing-by-synthesis and reversible dye-terminators that enable the identification of single bases are introduced into DNA strands and used to determine the series of base pairs in DNA.
Emiyu K, Lelisa K
openaire +1 more source
Monitoring Error Rates In Illumina Sequencing [PDF]
Journal of Biomolecular Techniques : JBT, 2016 Guaranteeing high-quality next-generation sequencing data in a rapidly changing environment is an ongoing challenge. The introduction of the Illumina NextSeq 500 and the depreciation of specific metrics from Illumina's Sequencing Analysis Viewer (SAV; Illumina, San Diego, CA, USA) have made it more difficult to determine directly the baseline error ...
Leigh J, Manley +2 more
openaire +2 more sources
Characterization of pseudorabies virus transcriptome by Illumina sequencing [PDF]
BMC Microbiology, 2015 Pseudorabies virus is a widely-studied model organism of the Herpesviridae family, with a compact genome arrangement of 72 known coding sequences. In order to obtain an up-to-date genetic map of the virus, a combination of RNA-sequencing approaches were applied, as recent advancements in high-throughput sequencing methods have provided a wealth of ...
Oláh, Péter +5 more
openaire +4 more sources
Paired-end sequencing of Fosmid libraries by Illumina [PDF]
Genome Research, 2012 Eliminating the bacterial cloning step has been a major factor in the vastly improved efficiency of massively parallel sequencing approaches. However, this also has made it a technical challenge to produce the modern equivalent of the Fosmid- or BAC-end sequences that were crucial for assembling and analyzing complex genomes during the Sanger-based ...
Williams, Louise J.S. +12 more
openaire +2 more sources
PANDAseq: paired-end assembler for illumina sequences [PDF]
BMC Bioinformatics, 2012 Abstract Background Illumina paired-end reads are used to analyse microbial communities by targeting amplicons of the 16S rRNA gene. Publicly available tools are needed to assemble overlapping paired-end reads while correcting mismatches and uncalled bases; many errors could be corrected to obtain higher sequence ...
Andre P. Masella +4 more
openaire +4 more sources
BFC: correcting Illumina sequencing errors [PDF]
Bioinformatics, 2015 Abstract Summary: BFC is a free, fast and easy-to-use sequencing error corrector designed for Illumina short reads. It uses a non-greedy algorithm but still maintains a speed comparable to implementations based on greedy methods. In evaluations on real data, BFC appears to correct more errors with fewer overcorrections in comparison to ...
openaire +3 more sources