RAD

ESTbiobank-Microbiome

Some useful scripts for microbiome analysis (Whole genome sequencing data)

2022_Abundance-Prevalence.ipynb

• 🤗 To vizualize Abundance-Prevalence plot
• 🦠 Manualy made table with taxonomic information as input

2022_ReadsNumb_vs_ContigsStats.ipynb

• 🤗 To understand the impact of the number of reads on the quality of the assembly
• 🦠 Input files are the stats data were taken from MEGAHIT v1.2.9 log files after assemblies were done

2022_reads_number_Path.sh

• 🧬 Calculate the number of reads for all *.fq.gz files in the folder

2022_kraken_top_species.ipynb

• 🤗 For identification the most represented spesies in samples set with the biggest reads number per each sample
• 🦠 Input files are the output of kraken-report
• 💌 Output is the boxplot and a table
• 👋 You can change number of top species and per species reads threshhold

2022_kraken_top_rank.ipynb

• 🤗 For identification the most represented genus or other taxonomic rank among the metagenome samples
• 🦠 Input files are the output of kraken-report
• 💌 Output is the boxplot and a table
• 👋 You can change taxon rank and filtering level

2022_kraken_Phylum_microbiome_composition.ipynb

• 🤗 For identification most abundant Phylum in microbiomes across some cohort subjects
• 🦠 Input files are the output of kraken-report
• 💌 Output is the boxplot and a table
• 👋 You can caclulate reads number or reads percent

2022_kraken_Domain_microbiome_composition.ipynb

• 🤗 For identification Domain level microbiome composition across some cohort subjects
• 🦠 Input files are the output of kraken-report
• 💌 Output is the boxplot and a table
• 👋 You can caclulate reads number or reads percent