sgavril/bioinfo_notebook

I am using this repository to share some of my work notes, which includes system admin, data analysis methods, pipeline developments, example commands. I hope this can be useful for others.

Table of contents

• System administrator

  • How to install a M.2 NVMe SSD drive
  • Install Ubuntu, minKNOW, CUDA, and enable gpu based guppy basecalling
  • Install WSL2 on windows 10, and enable CUDA, gpu based guppy basecalling
  • Build cluster with slurm - step by step

• Genomics and Metagenomics

  • Pathogen whole genome sequence analysis pipeline
  • Metagenomics crash course
  • Eukaryotic metagenome annotation
  • Nanopore genome and metagenome sequence analysis

• SARS-Cov-2 data analysis

  • A pipeline used to identify inter and intra variants from illumina covid dataset

• Other tools

  • pcrValidator