Inferring selective constraint from population genomic data suggests recent regulatory turnover in the human brain [PDF]
, 2013 The comparative genomics revolution of the past decade has enabled the discovery of functional elements in the human genome via sequence comparison. While that is so, an important class of elements, those specific to humans, is entirely missed by searching for sequence conservation across species.
arxiv +1 more source
Sensitive Long-Indel-Aware Alignment of Sequencing Reads [PDF]
arXiv, 2013 The tremdendous advances in high-throughput sequencing technologies have made population-scale sequencing as performed in the 1000 Genomes project and the Genome of the Netherlands project possible. Next-generation sequencing has allowed genom-wide discovery of variations beyond single-nucleotide polymorphisms (SNPs), in particular of structural ...
arxiv
Estimation of genome size using k-mer frequencies from corrected long reads [PDF]
arXiv, 2020 The third-generation long reads sequencing technologies, such as PacBio and Nanopore, have great advantages over second-generation Illumina sequencing in de novo assembly studies. However, due to the inherent low base accuracy, third-generation sequencing data cannot be used for k-mer counting and estimating genomic profile based on k-mer frequencies ...
arxiv
COGEDAP: A COmprehensive GEnomic Data Analysis Platform [PDF]
arXiv, 2022 Non-sharable sensitive data collection and analysis in large-scale consortia for genomic research is complicated. Time consuming issues in installing software arise due to different operating systems, software dependencies and running the software. Therefore, easier, more standardized, automated protocols and platforms can be a solution to overcome ...
arxiv
The code of codes: scientific and social issues in the human genome project [PDF]
, 1993 Lesley A. Hall
openalex +3 more sources
Scaffolder - Software for Reproducible Genome Scaffolding. [PDF]
, 2011 Background: Assembly of short-read sequencing data can result in a fragmented non-contiguous series of genomic sequences. Therefore a common step in a genome project is to join neighboring sequence regions together and fill gaps in the assembly using ...
Hazel A. Barton, Michael D. Barton
core +1 more source
Discovery of Phylogenetic Relevant Y-chromosome Variants in 1000 Genomes Project Data [PDF]
arXiv, 2013 Current Y chromosome research is limited in the poor resolution of Y chromosome phylogenetic tree. Entirely sequenced Y chromosomes in numerous human individuals have only recently become available by the advent of next-generation sequencing technology. The 1000 Genomes Project has sequenced Y chromosomes from more than 1000 males.
arxiv
Baa.pl: A tool to evaluate de novo genome assemblies with RNA transcripts [PDF]
arXiv, 2013 Assessing the correctness of genome assemblies is an important step in any genome project. Several methods exist, but most are computationally intensive and, in some cases, inappropriate. Here I present baa.pl, a fast and easy-to-use program that uses transcript data to evaluate genomic assemblies.
arxiv
Genome sequencing project has begun on two plant trypanosomatids (Phytomonas) [PDF]
, 2010 Some trypanosomatids are responsible for wilt in tropical crops, such as hartrot disease in the coconut palm. They have a major economic impact in Latin America and the Caribbean.
Artiguenave, Françoise +9 more
core
The Chills and Thrills of Whole Genome Sequencing [PDF]
arXiv, 2013 In recent years, Whole Genome Sequencing (WGS) evolved from a futuristic-sounding research project to an increasingly affordable technology for determining complete genome sequences of complex organisms, including humans. This prompts a wide range of revolutionary applications, as WGS promises to improve modern healthcare and provide a better ...
arxiv