• Skip to main content
  • Skip to top navigation bar
  • Skip to What's New

    @ github

    What's New

    Recent papers:

    Daniel S Standage, Tim Lai & Volker P Brendel (2022) iLoci: Robust evaluation of genome content and organization for provisional and mature genome assemblies. Nucleic Acids Research Genomics and Bioinformatics 4, Issue 1, March 2022, lqac013, https://doi.org/10.1093/nargab/lqac013 [PubMed ID: 35211671] [online article] [PDF]

    Morandin, C., Brendel, V.P., Sundström, L.; Helanterä, H. & Mikheyev, A. (2019) Changes in gene DNA methylation and expression networks accompany caste specialization and age-related physiological changes in a social insect methylation. Molecular Ecology, 28, 1975-1993. [PubMed ID: 30809873] [online article] [PDF]

    The future of computational genomics:

      Brendel, V.P. (2018) From small RNA discoveries to a new paradigm in computational genomics? New Phytol. 220, 659-660. [PubMed ID: 30324739] [online article] [PDF]

    Check out our github site!


    PlantGDB News:

    Brendel Group - SingularityHub

    What does our "SingularityHub" page offer? We are a computational genomics group and support containers for software in this realm. Typically, the containers bundle multiple packages of diverse programs that are frequently used in combination in a project. In our own work, we seek to bundle everything that should be referenced in the methods description of our scientific papers, thus ensuring complete technical reproducibility of the computational work. For usage instructions and a complete list of all available containers, please see our bgSingularityHub github repository and CATALOG page, respectively.

    DNA methylation analysis workflows

    BWASP: [ bwasp.sif BWASP-archive] BWASPR: [bwaspr.sif BWASPR-archive]

    Genome assembly and analysis

    SRAssembler: [sra.sif SRAassembler-archive] AllRice: [AllRice.sif AllRice-archive] DiscovarDeNovo: [DDN.sif DDN-archive] GoSTRIPES: [GoSTRIPES.sif GoSTRIPES-archive] SNPat: [SNPat.sif SNPat-archive] TSRchitect: [tsr.sif TSRchitect-archive]


    mRNAmarkup: [mRNAmarkup.sif mRNAmarkup-archive]

    Teaching tools

    FMAB: [FMAB.sif FMAB-archive]