Genom-Analysis

This repository contains my bioinformatics workflows for genome and transcriptome analysis of Streptomyces rimosus strains R7 (wild-type) and HP126 (hyperproducer).

Project overview

• De novo genome assembly and polishing (Flye + Pilon)
• Quality control of Illumina and Nanopore reads (FastQC, MultiQC)
• Genome comparison and functional annotation (QUAST, BUSCO, MUMmer, Prokka, eggNOG-mapper)
• RNA-seq differential expression analysis (DESeq2)

Tools and technologies

• Programming: Python, Bash, R
• HPC: UPPMAX (Rackham, Slurm)
• Software: Flye, Pilon, Prokka, eggNOG-mapper, QUAST, BUSCO, MUMmer, DESeq2

Repository structure

• code/ – scripts and pipelines used in the analysis
• author/ – project-related information and notes
• out/ – selected output files and summary results (no raw data)

Status

This project is part of my Bioinformatics MSc work and will be updated as I refine the analysis and documentation.