Service documentation - BU-ISCIII/BU-ISCIII GitHub Wiki

Introduction

BU-ISCIII offers a bunch of services determined in its Service portfolio with fixed input and output. The pipelines developed offer standard analysis for different experiments of next generation sequencing data involving human and microbial research. In order to get access to this pipelines users have three possibilities:

  • Ask for a service: we will download the data and perform the analysis making a delivery of the results and an analysis report.
  • Do it yourself asking for a Virtual Machine or HPC access and following each service documentation (linux and bioinformatics skills required.)
  • Do it yourself using our galaxy server implementation (Coming soon)

Services available

Bioinformatics counseling

  • Bioinformatics analysis consulting: just ask us for a consulting service using iSkyLIMS, and we will set up a meeting. We will try to guide you with any NGS experiment or bioinformatic analysis design using our expertise.

  • In-house and outer course organization: if you want to organize any training activity we can offer you our expertise and training material as teachers or co-organizers.

  • Student training/internship: BU-ISCIII offers the possibility of training internships in our lab. This internships can offer you access to our infrastructure and expertise, involving yourself in a bioinformatic research environment. Internships must have minimum a 3 month extension and the following requirements:

    • Master thesis: if you are a student interested in developing your Master thesis with us..

      • You must be involved in a MSc related to bioinformatics or computational biology.
      • Your University/study center must have a agreement with the ISCIII (contact us to get this information)
      • You have to develop a Master thesis in the internship period, please contact us with your cv and your research interest so we can involve you in the best possible project.

    • Research internship: if you are a researcher and you want to make an training internship with us, or you have a project that involves NGS data analysis and you need help in your analysis you need..

      • Contact us with a research project in which you describe the experiment you have/want to perform, and the results you expect to get from the bioinformatic analysis.
      • In order to obtain the best outcomes from the internship a collaboration will be created between the research group and BU-ISCIII focusing on getting both groups best interests.

User support

  • Installation and support of bioinformatic software on Linux OS: if you have a linux machine we can support you in the installation of bioinformatics software.

  • Installation and access to Virtual machines in the Unit server containing bioinformatic software: if you want to perform your own analysis but you don't have enough computing resources, BU-ISCIII offers you the access to a virtual machine with custom bioinformatic software installation.

  • Code snippets development: small code snippets development is offered to ISCIII researchers to perform small analysis like concatenating big files, iteration through many samples,

Genomic data analysis

  • Trio/family variant calling

    • Description
    • Pipeline repo
    • Results report

  • Variant calling and annotation

    • Description
    • Pipeline repo
    • Results report

  • Microbial: Whole genome outbreak analysis

    • Description
    • Pipeline repo
    • Results report

  • Microbial: wgMLST

    • Description
    • Pipeline repo
    • Results report

  • Microbial: MLST + virulence + AMR + plasmid analysis

    • Description
    • Pipeline repo
    • Results report

  • Microbial: Assembly + automatic annotation

    • Description
    • Pipeline repo
    • Results report

  • Microbial: plasmidID pipeline - strain plasmid characterization

    • Description
    • Pipeline repo
    • Results report

  • miRNA-Seq analysis

    • Description
    • Pipeline repo
    • Results report

  • mRNA-Seq analysis

    • Description
    • Pipeline repo
    • Results report

  • Low frequency variant detection

    • Description
    • Pipeline repo
    • Results report

  • Viral: assembly and minor variants detection

    • Description
    • Pipeline repo
    • Results report

  • 16S taxonomic profiling

    • Description
    • Pipeline repo
    • Results report

  • Shotgun metagenomics

    • Description
    • Pipeline repo
    • Results report

  • Peak detection and annotation

    • Description
    • Pipeline repo
    • Results report

  • SARS-CoV-2 Serivce