sarsaparella / projects_bi_2022

Bioinformatics Institute educational projects

This repository contains all projects that I made throught my one-year training program at Bioinformatics Institute (Sept 2022 - June 2023).

Each project folder contains a lab notebook and a small paper that I wrote based on the results.

Here is the list of all projects:

• What causes antibiotic resistance? Alignment to reference, variant calling.

  Tools: FastQC, Trimmomatic, BWA-MEM, samtools, VarScan, snpEff

• “Why did I get the flu?”. Deep sequencing, error control, p-value, viral evolution.

  Tools: Snakemake, BWA-MEM, samtools, VarScan, awk

• E.coli 2011 outbreak investigation.

  Tools: SPAdes, jellyfish, QUAST, prokka, ResFinder, Mauve

• Tardigrades: from genestealers to space marines (my fav ^^)

  New bioinformatics skills covered: gene prediction, functional annotation, protein localization

  Tools: AUGUSTUS, Diamond, WoLF PSORT, TargetP 1.1 Server, HMMER

• H+, or how to build a perfect human.

  Tools and databases: plink, MtDNA_tools, Y-DNA_tools, VEP (Variant Effect Predictor), dbSNP, SNPedia, OMIM

• Baking Bad: Differential RNA expression analysis

  New bioinformatics skills covered: splice-junction aware alignment, guided transcript assembly, differential expression analysis

  Tools: HISAT2, Deseq2, gffread,

• Dead Man’s Teeth. Introduction to metagenomics analysis.

  New bioinformatics skills covered: 16S vs whole metagenome, alignment, ASV clustering.

  Tools: QIIME2, samtools, BWA-MEM, BEDtools

Be ware, all projects were made in tight deadlines and meant to be purely educational, so some mistakes are very much possible (っ˘̩╭╮˘̩)っ