QQ-SNV: single nucleotide variant detection at low frequency by comparing the quality quantiles [PDF]
, 2015 Background: Next generation sequencing enables studying heterogeneous populations of viral infections. When the sequencing is done at high coverage depth ("deep sequencing"), low frequency variants can be detected.
Aerssens, Jeroen +7 more
core +4 more sources
16S rRNA gene sequencing of mock microbial populations- impact of DNA extraction method, primer choice and sequencing platform [PDF]
, 2016 peer-reviewedBackground Next-generation sequencing platforms have revolutionised our ability to investigate the microbiota composition of complex environments, frequently through 16S rRNA gene sequencing of the bacterial component of the
Claesson, Marcus J. +4 more
core +2 more sources
Diversity of immunoglobulin light chain genes in non-teleost ray-finned fish uncovers IgL subdivision into five ancient isotypes [PDF]
, 2018 The aim of this study was to fill important gaps in the evolutionary history of immunoglobulins by examining the structure and diversity of IgL genes in non-teleost ray-finned fish.
Andreyushkova, Daria A +14 more
core +5 more sources
Shifting Feeding Habits During Settlement Among Small Yellow Croakers (Larimichthys polyactis)
Frontiers in Marine Science, 2022 The small yellow croaker, Larimichthys polyactis, is a keystone species in the Yellow Sea and the East China Sea, with significant impacts on the regional ecosystem, but has experienced decades of population decline as a result of environmental changes ...
Yuange Chen +4 more
doaj +1 more source
Spaced seeds improve k-mer-based metagenomic classification [PDF]
, 2015 Metagenomics is a powerful approach to study genetic content of environmental samples that has been strongly promoted by NGS technologies. To cope with massive data involved in modern metagenomic projects, recent tools [4, 39] rely on the analysis of k ...
Brinda, Karel +2 more
core +2 more sources
CD-HIT-OTU-MiSeq, an Improved Approach for Clustering and Analyzing Paired End MiSeq 16S rRNA Sequences [PDF]
, 2017 AbstractIn recent years, Illumina MiSeq sequencers replaced pyrosequencing platforms and became dominant in 16S rRNA sequencing. One unique feature of MiSeq technology, compared with Pyrosequencing, is the Paired End (PE) reads, with each read can be sequenced to 250-300 bases to cover multiple variable regions on the 16S rRNA gene.
Li, Weizhong, Chang, Yuanyuan
openaire +1 more source
Cost-efficient high-throughput HLA typing by MiSeq amplicon sequencing [PDF]
BMC Genomics, 2014 Abstract Background A close match of the HLA alleles between donor and recipient is an important prerequisite for successful unrelated hematopoietic stem cell transplantation. To increase the chances of finding an unrelated donor, registries recruit many hundred thousands of volunteers each ...
Lange, Vinzenz +15 more
openaire +2 more sources
mockrobiota: a Public Resource for Microbiome Bioinformatics Benchmarking. [PDF]
, 2016 Mock communities are an important tool for validating, optimizing, and comparing bioinformatics methods for microbial community analysis. We present mockrobiota, a public resource for sharing, validating, and documenting mock community data resources ...
Arron Shiffer +10 more
core +6 more sources
The complete mitogenome of Caridina indistincta ‘sp. A’ (Decapoda: Atyidae)
Mitochondrial DNA. Part B. Resources, 2018 A complete mitochondrial genome sequence was determined for a member of the Caridina indistincta species complex known as C. indistincta ‘sp. A’. The 15,461 bp sequence (GenBank: MH189850) was obtained via genome skimming, and contains 13 protein coding ...
Daniel J. Schmidt
doaj +1 more source
Frontiers in Microbiology, 2023 Culture-independent metagenomic sequencing of enriched agricultural water could expedite the detection and virulotyping of Shiga toxin-producing Escherichia coli (STEC).
Meghan Maguire +7 more
doaj +1 more source