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:
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What causes antibiotic resistance? Alignment to reference, variant calling.
Tools: FastQC, Trimmomatic, BWA-MEM, samtools, VarScan, snpEff
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“Why did I get the flu?”. Deep sequencing, error control, p-value, viral evolution.
Tools: Snakemake, BWA-MEM, samtools, VarScan, awk
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E.coli 2011 outbreak investigation.
Tools: SPAdes, jellyfish, QUAST, prokka, ResFinder, Mauve
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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
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H+, or how to build a perfect human.
Tools and databases: plink, MtDNA_tools, Y-DNA_tools, VEP (Variant Effect Predictor), dbSNP, SNPedia, OMIM
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Baking Bad: Differential RNA expression analysis
New bioinformatics skills covered: splice-junction aware alignment, guided transcript assembly, differential expression analysis
Tools: HISAT2, Deseq2, gffread,
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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