Correcting Illumina data [PDF]
Briefings in Bioinformatics, 2014 Next-generation sequencing technologies revolutionized the ways in which genetic information is obtained and have opened the door for many essential applications in biomedical sciences. Hundreds of gigabytes of data are being produced, and all applications are affected by the errors in the data. Many programs have been designed to correct these errors,
Michael Molnar, Lucian Ilie
openaire +2 more sources
Illumina reads correction: evaluation and improvements
Scientific Reports, 2023 Abstract The paper focuses on the correction of Illumina WGS sequencing reads. We provide an extensive evaluation of the existing correctors. To this end, we measure an impact of the correction on variant calling (VC) as well as de novo assembly. It shows, that in selected cases read correction improves the VC results quality. We also
Maciej Długosz, Sebastian Deorowicz
openaire +3 more sources
An Illumina metabarcoding pipeline for fungi [PDF]
Ecology and Evolution, 2014 AbstractHigh‐throughput metabarcoding studies on fungi and other eukaryotic microorganisms are rapidly becoming more frequent and more complex, requiring researchers to handle ever increasing amounts of raw sequence data. Here, we provide a flexible pipeline for pruning and analyzing fungal barcode (ITS rDNA) data generated as paired‐end reads on ...
Bálint, Miklós +4 more
openaire +3 more sources
Error rate for imputation from the Illumina BovineSNP50 chip to the Illumina BovineHD chip [PDF]
Genetics Selection Evolution, 2014 Imputation of genotypes from low-density to higher density chips is a cost-effective method to obtain high-density genotypes for many animals, based on genotypes of only a relatively small subset of animals (reference population) on the high-density chip.
Schrooten, Chris +9 more
openaire +7 more sources
Species identification and profiling of complex microbial communities using shotgun Illumina sequencing of 16S rRNA amplicon sequences. [PDF]
, 2013 The high throughput and cost-effectiveness afforded by short-read sequencing technologies, in principle, enable researchers to perform 16S rRNA profiling of complex microbial communities at unprecedented depth and resolution. Existing Illumina sequencing
Niranjan Nagarajan +23 more
core +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
Illuminating Choices for Library Prep: A Comparison of Library Preparation Methods for Whole Genome Sequencing of Cryptococcus neoformans Using Illumina HiSeq. [PDF]
, 2014 The industry of next-generation sequencing is constantly evolving, with novel library preparation methods and new sequencing machines being released by the major sequencing technology companies annually.
Mathew A Beale +14 more
core +1 more source
Short read Illumina data for the de novo assembly of a non-model snail species transcriptome (Radix balthica, Basommatophora, Pulmonata), and a comparison of assembler performance [PDF]
, 2011 Background: Until recently, read lengths on the Solexa/Illumina system were too short to reliably assemble transcriptomes without a reference sequence, especially for non-model organisms.
Wheat, Christopher W. +10 more
core +2 more sources
, 2021 Nextflow DSL 2; SPAdes 3.15.1; assemble plasmids with metaplasmidSPAdes and verify them using ViralVerify (optional); minor changes; more ...
Davide Albanese
core +1 more source