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mahesh-panchal/README.md

Hi 👋, I'm Mahesh Binzer-Panchal

A bioinformatician working for the National Bioinformatics Infrastructure Sweden.

I support research groups by performing bioinformatic analyses and developing workflows on request. My bioinformatic expertise focuses on de novo genome assembly, but I am also able to perform other sequence based analyses, such as variant calling, amplicon analysis, ancient DNA analysis, and more. In addition to my support work, I'm currently helping develop a genome assembly and annotation workflow for the Swedish Pilot Project in the Earth Biogenome Project. As part of my support work, I aim to make my work reproducible, using version control, workflow managers, and containerized software. I use this template as the starting point for my work, keeping data, files, and code organised, and hopefully easy to follow and extend for those I support.

I'm adept at programming, and writing workflows in particular. I'm well versed in Bash scripting, as well being able to use Perl, awk, sed, and R too. I write workflows using the Nextflow workflow language, based on Groovy. I have used various other languages in the past including Java, C, C++, Turing, Haskell, Prolog, and Assembly, including database languages such as PostgresQL. I'm familiar with various markup and serialization languages such as Markdown, HTML, Wiki Markup, Latex, and YAML. In my work, I regularity use Git, Docker, and Singularity, as well as Github Actions and Makefiles for automation, and Gitpod as a development environment.

Nextflow and nf-core

I contribute to the nf-core and Nextflow community, helping answer questions and develop best-practice workflows.

Expand for my notable contributions

Teaching

I am a certified Carpentries Instructor. I have helped develop The Carpentries Introduction to Nextflow.

Languages and Tools:

As a bioinformatician, I use a variety of tools to aid my work. These are tools I have used in recent years.

mindmap
  root((Tools))
    Programming Languages
      Bash
      Awk
      Nextflow/Groovy
      R
      Perl
      SQL
      Jq
      Python
    Package management
      Conda/Mamba
      Docker
      Singularity/Apptainer
      Virtual env
      Modules
    Version control
      Git
      Github
    Markup
      Markdown
      Latex
      Wikitext
      HTML
    Diagramming
      Mermaid
    Literate programming
      Quarto
      RMarkdown
    Project management
      Github
      Trello
      Confluence
      Notion
    Automation
      Github actions
      Make
      Nextflow
      Quarto
    Developer environments
      MacOs
      Linux
      Gitpod
      HPC

mahesh-panchal

 mahesh-panchal

Pinned

  1. NBIS_project_template NBIS_project_template Public template

    Personal template for making and describing how to do reproducible NBIS support projects

    Nextflow 7 1

  2. ANeCA ANeCA Public

    ANeCA: Automated Nested Clade Analysis

    Java

  3. NBISweden/pipelines-nextflow NBISweden/pipelines-nextflow Public

    A set of workflows written in Nextflow for Genome Annotation.

    Nextflow 42 18

  4. NBISweden/Earth-Biogenome-Project-pilot NBISweden/Earth-Biogenome-Project-pilot Public

    Assembly and Annotation workflows for analysing data in the Earth Biogenome Project pilot project.

    Nextflow 9 6

  5. reproducible-research reproducible-research Public

    A demonstration of how to work reproducibly using version control, containers, and a workflow manager.

    Nextflow 1 2