evangelosmourkas/MRC-CLIMB_Workshop_Gambia

This repository represents a showcase of Jupyter Notebooks, presented during the CLIMB-BIG-DATA Bioinformatics Workshop at the MRC Unit in The Gambia. The workshop is taking place between November 13th and 17th, 2023. # MRC-CLIMB_Workshop_Gambia This repository represents a showcase of Jupyter Notebooks, presented during the CLIMB-BIG-DATA Bioinformatics Workshop at the MRC Unit in The Gambia. The workshop took place in the MRC Unit in Fajara between the 13th and 17th of November 2023. ## Publication Genomes and reads associated with this show-case tutorial is linked to the following publication: "Gene pool transmission of multidrug resistance among _Campylobacter_ from livestock, sewage and human disease" published in Environmental Microbiology (doi:10.1111/1462-2920.14760). All sequence data are linked to NCBI BioProject PRJNA528879. The bacterial genomes are available in GenBank under accession codes SRX5575129 to SRX5587545. ## Files Summary The files include data for 169 isolates representing a collection sampled from human clinical cases, animals and sewage: Each directory contains the following: * **Raw_Reads**: directory with raw reads data (currently available on NCBI BioProject PRJNA528879 - will be available on figshare) * **Assemblies**: directory with assemblies (available on figshare) * **Core_alignment.fas**: Core alignment of 169 assembled genomes (available on figshare) * **Phylogeny.nwk**: Maximum-likelihood tree reconstructed by FastTree * **Metadata.csv**: Genome metadata .csv file used for visualization * **Figshare_DOI.txt**: File with doi links to data repositories in figshare * **Antimicrobial_resistance_PA.xlsx**: Presence absence of AMR genes ## Software and packages * SPAdes v3.15.5 * checkM v1.1.6 * Snippy 4.4.3 * MLST v2.23.0 * PIRATE * RAxML v8.2.11 * Abricate ## R packages * ggplot2 * ggtree * ape # Workflow ## Reads assembly (with SPAdes) ``` spades.py –12 short_read_files –phred-offset 33 -o output_directory ``` ## Genome quality control (with checkM) ``` checkm lineage_wf -t 30 -x fas ./contigs/ /home/ubuntu/Output_directory ``` ## Assigning MLST using pubMLST schemes ``` mlst genome.fas ``` ## Generating a core genome alignment ``` snippy - …