Impact of reduced-representation sequencing protocols on detecting population structure in a threatened marsupial
Sign Up to like & getrecommendations! Published in 2019 at "Molecular Biology Reports"
DOI: 10.1007/s11033-019-04966-6
Abstract: Reduced-representation sequencing methods have wide utility in conservation genetics of non-model species. Several methods are now available that reduce genome complexity to examine a wide range of markers in a large number of individuals. We… read more here.
Keywords: reduced representation; population; representation sequencing; population structure ... See more keywords
A comprehensive evaluation of alignment software for reduced representation bisulfite sequencing data
Sign Up to like & getrecommendations! Published in 2018 at "Bioinformatics"
DOI: 10.1093/bioinformatics/bty174
Abstract: Motivation The rapid development of next-generation sequencing technology provides an opportunity to study genome-wide DNA methylation at single-base resolution. However, depletion of unmethylated cytosines brings challenges for aligning bisulfite-converted sequencing reads to a large reference.… read more here.
Keywords: methylation; cpg sites; reduced representation; rrbssim ... See more keywords
DepthFinder: a tool to determine the optimal read depth for reduced-representation sequencing
Sign Up to like & getrecommendations! Published in 2020 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btz473
Abstract: MOTIVATION Identification of DNA sequence variations such as single nucleotide polymorphisms (SNPs) is a fundamental step towards genetic studies. Reduced-representation sequencing methods have been developed as alternatives to whole genome sequencing to reduce costs and… read more here.
Keywords: read depth; depthfinder; representation sequencing; tool ... See more keywords
epiGBS2: Improvements and evaluation of highly multiplexed, epiGBS-based reduced representation bisulfite sequencing.
Sign Up to like & getrecommendations! Published in 2022 at "Molecular ecology resources"
DOI: 10.1111/1755-0998.13597
Abstract: Several reduced representation bisulfite sequencing methods have been developed in recent years to determine cytosine methylation de novo in non-model species. Here, we present epiGBS2, a laboratory protocol based on epiGBS (Gurp et al., 2016)… read more here.
Keywords: pipeline; reduced representation; representation bisulfite; bisulfite sequencing ... See more keywords
Discovery of thermophilic Bacillales using reduced-representation genotyping for identification
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DOI: 10.1186/s12866-020-01800-z
Abstract: This study demonstrates the use of reduced-representation genotyping to provide preliminary identifications for thermophilic bacterial isolates. The approach combines restriction enzyme digestion and PCR with next-generation sequencing to provide thousands of short-read sequences from across… read more here.
Keywords: reduced representation; microbiology; identification; genome ... See more keywords