Development of polymorphic microsatellites for genetic studies of white scar oyster (Crassostrea belcheri) using paired-end shotgun sequencing.
Sign Up to like & getrecommendations! Published in 2021 at "Molecular biology reports"
DOI: 10.1007/s11033-021-06442-6
Abstract: White scar oyster Crassostrea belcheri is a commercially important bivalve species in Thailand. Appropriate genetic markers are needed for effective management to elevate its production efficiency. Type II microsatellites of C. belcheri were identified and… read more here.
Keywords: white scar; oyster crassostrea; belcheri; paired end ... See more keywords
Compositional Bias in Naïve and Chemically-modified Phage-Displayed Libraries uncovered by Paired-end Deep Sequencing
Sign Up to like & getrecommendations! Published in 2018 at "Scientific Reports"
DOI: 10.1038/s41598-018-19439-2
Abstract: Understanding the composition of a genetically-encoded (GE) library is instrumental to the success of ligand discovery. In this manuscript, we investigate the bias in GE-libraries of linear, macrocyclic and chemically post-translationally modified (cPTM) tetrapeptides displayed… read more here.
Keywords: end deep; deep sequencing; paired end; bias ... See more keywords
Long fragments achieve lower base quality in Illumina paired-end sequencing
Sign Up to like & getrecommendations! Published in 2019 at "Scientific Reports"
DOI: 10.1038/s41598-019-39076-7
Abstract: Illumina’s technology provides high quality reads of DNA fragments with error rates below 1/1000 per base. Sequencing runs typically generate millions of reads in which the vast majority of the reads has an average error… read more here.
Keywords: quality; paired end; end sequencing; base ... See more keywords
IMperm: a fast and comprehensive IMmune Paired-End Reads Merger for sequencing data
Sign Up to like & getrecommendations! Published in 2023 at "Briefings in bioinformatics"
DOI: 10.1093/bib/bbad080
Abstract: The adaptive immune receptor repertoire (AIRR), consisting of T- and B-cell receptors, is the core component of the immune system. The AIRR sequencing is commonly used in cancer immunotherapy and minimal residual disease (MRD) detection… read more here.
Keywords: sequencing data; paired end; end reads; merger sequencing ... See more keywords
A Bayesian model integration for mutation calling through data partitioning
Sign Up to like & getrecommendations! Published in 2019 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btz233
Abstract: Abstract Motivation Detection of somatic mutations from tumor and matched normal sequencing data has become among the most important analysis methods in cancer research. Some existing mutation callers have focused on additional information, e.g. heterozygous… read more here.
Keywords: information; model integration; paired end; model ... See more keywords
Hybrid-denovo: a de novo OTU-picking pipeline integrating single-end and paired-end 16S sequence tags
Sign Up to like & getrecommendations! Published in 2018 at "GigaScience"
DOI: 10.1093/gigascience/gix129
Abstract: Abstract Background Illumina paired-end sequencing has been increasingly popular for 16S rRNA gene-based microbiota profiling. It provides higher phylogenetic resolution than single-end reads due to a longer read length. However, the reverse read (R2) often… read more here.
Keywords: end single; end; hybrid denovo; paired end ... See more keywords
An optimized approach for local de novo assembly of overlapping paired-end RAD reads from multiple individuals
Sign Up to like & getrecommendations! Published in 2018 at "Royal Society Open Science"
DOI: 10.1098/rsos.171589
Abstract: Restriction site-associated DNA (RAD) sequencing is revolutionizing studies in ecological, evolutionary and conservation genomics. However, the assembly of paired-end RAD reads with random-sheared ends is still challenging, especially for non-model species with high genetic variance.… read more here.
Keywords: optimized approach; rad; paired end; rad reads ... See more keywords
ISEA: Iterative Seed-Extension Algorithm for De Novo Assembly Using Paired-End Information and Insert Size Distribution
Sign Up to like & getrecommendations! Published in 2017 at "IEEE/ACM Transactions on Computational Biology and Bioinformatics"
DOI: 10.1109/tcbb.2016.2550433
Abstract: The purpose of de novo assembly is to report more contiguous, complete, and less error prone contigs. Thanks to the advent of the next generation sequencing (NGS) technologies, the cost of producing high depth reads… read more here.
Keywords: seed; novo assembly; paired end; end information ... See more keywords
NGmerge: merging paired-end reads via novel empirically-derived models of sequencing errors
Sign Up to like & getrecommendations! Published in 2018 at "BMC Bioinformatics"
DOI: 10.1186/s12859-018-2579-2
Abstract: BackgroundAdvances in Illumina DNA sequencing technology have produced longer paired-end reads that increasingly have sequence overlaps. These reads can be merged into a single read that spans the full length of the original DNA fragment,… read more here.
Keywords: quality; merging programs; paired end; end reads ... See more keywords
METAMVGL: a multi-view graph-based metagenomic contig binning algorithm by integrating assembly and paired-end graphs
Sign Up to like & getrecommendations! Published in 2021 at "BMC Bioinformatics"
DOI: 10.1186/s12859-021-04284-4
Abstract: Background Due to the complexity of microbial communities, de novo assembly on next generation sequencing data is commonly unable to produce complete microbial genomes. Metagenome assembly binning becomes an essential step that could group the… read more here.
Keywords: multi view; contig binning; graph; paired end ... See more keywords
Can Targeting Non-Contiguous V-Regions With Paired-End Sequencing Improve 16S rRNA-Based Taxonomic Resolution of Microbiomes?: An In Silico Evaluation
Sign Up to like & getrecommendations! Published in 2019 at "Frontiers in Genetics"
DOI: 10.3389/fgene.2019.00653
Abstract: Background: Next-generation sequencing (NGS) technologies have enabled probing of microbial diversity in different environmental niches with unprecedented sequencing depth. However, due to read-length limitations of popular NGS technologies, 16S amplicon sequencing-based microbiome studies rely on… read more here.
Keywords: paired end; end sequencing; 16s rrna; taxonomic resolution ... See more keywords