Essays about: "Snakemake"

Found 5 essays containing the word Snakemake.

  1. 1. Nanometa Live : A real-time metagenomic analysis pipeline and interface for species classification and pathogen characterization

    University essay from Högskolan i Skövde/Institutionen för biovetenskap

    Author : Kristoffer Sandås; [2023]
    Keywords : ;

    Abstract : Metagenomics studies the totality of genomes of all species in a microbial community. It is a young, growing field with medical, industrial, and ecological applications. Abundant metagenomic data is being produced today, but there is a lack of interpretation and visualization tools. READ MORE

  3. 2. Detecting structural variants in the DNA of the inbred Scandinavian wolf

    University essay from Uppsala universitet/Institutionen för biologisk grundutbildning

    Author : Lars Huson; [2023]
    Keywords : animal; animal population; bioinformatics; biological sciences; biology; Canis lupus; CNV; conservation genetics; conservation genomics; copy-number variation; DNA; endangered population; endangered species; evolution; evolutionary biology; extinction; genetic diversity; genetics; genetic variation; genomes; genomics; grey wolf; inbreeding; inbreeding depression; indel; mutation; pedigree; population genetics; population genomics; Scandinavia; smoove; snakemake; structural variant; SV; wolf; wolves;

    Abstract : Only 40 years ago, just three individuals made the journey from Finland/Russia to found the current wolf population in the southwest of Sweden. This population, that to this date descends from less than 10 founders, has a substantial increased extinction risk due to inbreeding. READ MORE

  4. 3. Developing saddleback and emperor tamarin SNP set for in situ genotyping

    University essay from Uppsala universitet/Institutionen för ekologi och genetik; Uppsala universitet/Institutionen för biologisk grundutbildning

    Author : Samantha López Clinton; [2022]
    Keywords : SNP genotyping; GT-Seq; conservation genomics; saddleback tamarin; emperor tamarin; Genotipado por SNPs; GT-seq; genómica para la conservación; pichico común; pichico emperador;

    Abstract : Many countries in the global south - which harbour the majority of the world’s biodiversity - face serious resource limitations and a lack of access to affordable sequencing services. Furthermore, biodiversity research and monitoring of non-model, threatened and/or cryptic species often relies on low-quality non-invasive genetic samples. READ MORE

  5. 4. Demography of Birch Populations across Scandinavia

    University essay from Uppsala universitet/Växtekologi och evolution; Uppsala universitet/Institutionen för biologisk grundutbildning

    Author : Janek Sendrowski; [2022]
    Keywords : birch; betula; pubescens; pendula; betula pubescens; betula pendula; silver birch; downy birch; demography; population structure; distribution of fitness effects; DFE; dadi; UMAP; PCA; ADMIXTURE; polyDFE; ice age; glaciation; tree; boreal forest; climate change; adaption; tetraploid; diploid-tetraploid introgression; Scandinavia; genetic cluster; pipeline; snakemake; bioinformatics; reproducible; population genetics; postglacial population expansion; demographic history; FEEMS; site-frequency spectrum; SFS; last glacial maximum; LGM; workflow; python; population expansion; population growth; EST-SFS; 0-fold degenerate; 4-fold degenerate; maximum likelihood estimation; MLE; variant call format; VCF; single-nucleotide polymorphism; SNP;

    Abstract : Boreal forests are particularly vulnerable to climate change, experiencing a much more drastic increase in temperatures and having a limited amount of more northern refugia. The trees making up these vast and important ecosystems already had to adapt previously to environmental pressures brought about by the repeated glaciations during past ice ages. READ MORE

  6. 5. ARG-MATEE Automated Pipeline for Detection of Antimicrobial Resistance in WGS Data Collected from Pig Farms and Surrounding Communities

    University essay from Uppsala universitet/Institutionen för biologisk grundutbildning

    Author : Holly Halstead; [2020]
    Keywords : Bioinformatics; Microbiology; Pipeline; Snakemake; ARG-MATEE; Antimicrobial Resistance; Pig Farms; Conda; iss virulence gene; Thailand; surveillance; escherichia coli; E. coli; klebsiella pneumoniae; One Health;

    Abstract : As part of recognizing the interconnected nature of different sectors in relation to health, AMR (antimicrobial resistance) has emerged as an issue of high global importance. E. coli isolates were taken from pig farms in Thailand, which serves as a point of interest in the study of ARGs (antimicrobial resistance genes) in emerging economies. READ MORE