This encompasses 2 projects
- Genome Assembly & Downstream Analysis of 192 Bacteriodetes strains
- generate_adapter_files.py - generate FASTA adapter files for trimmomatic
- genome_assembly_pipeline.sh - self-descriptive, preprocesses reads, assembles genome with SPades
- preparing_contigs_db.sh - preprocessing for Anv'io
- anvio_pangenomic.sh - performing pangenomic analysis in Anv'io
- add_zero.py - helper script to reformat files
- run_kraken_all.sh - helper script for running kraken2
- run_prokka_all.sh - helper script for genome annotation
- Quantitifying Presence of Mycobacterium Tuberculosis in 108 Pediatric Fecal Samples
- kraken2_bowtie.sh - filter raw reads & analyse with kraken2
- extract_reads.sh - extract reads classified as TB by Kraken2
- count_k_reads.py - helper script to count reads mapped to mtb by kraken2
- multiple_blast_queries.sh - BLAST extracted reads
- parse_blast_output.py - parse blast output from samples