Project 2

In this exercise we will examine one of the clades of Acinetobacter baumannii that the text of the paper says is related to another set of isolates sequenced in Kuwait.

Step 1: Examine Figure 5 in the paper

Figure 5 describes several organisms. The phylogenetic trees presented represent clusters of related isolates. The s6 cluster for Acinetobacter baumannii is described in the paper as being related to isolates from another study.

Step 2: Obtain the cluster s6 genomes from the hybrid assembly file.

We've done this task for you because it is complex, time consuming, and illustrates a problem with the way data is included from many papers today. o get the dataset to do further analysis, we've created a separate page listing what we did: Project 2: Step 2: Get S6 Genomes.

mkdir -p ~/project2/step2
cd ~/project2/step2

First get list of isolates in cluster 6

git clone https://github.com/csb5/hospital_microbiome.git
cd hospital_microbiome/output_tables
grep s6 strain_cluster_summary.tsv | grep Acinetobacter | cut -f3 >../../s6.nanopore.ids

#### Get the assemblies in bulk from the figshare site
```bash
    ## genome files are available at figshare, we will grab some of them
    wget https://ndownloader.figshare.com/files/21229971
    tar -xvzf 21229971

    ## assembly info file
    wget https://ndownloader.figshare.com/files/21229929
    mv 21229929 hybrid_assembly_genome_info.tab

    # translate "nanopore.ids" to assembly filenames
    fgrep -f s6.nanopore.ids hybrid_assembly_genome_info.tab |  cut -f1 >s6.genome.ids
    
    # copy out the assemblies of interest
    mkdir s6
    for i in `cat s6.genome.ids`
    do
        mv home/bertrandd/PROJECT_LINK/OPERA_LG/HOSPITAL_MICROBIOME/assembly_db/hybrid_assembly_genomes/$i.fa s6
    done
    
    # clean up excess assemblies
    rm -r home

Step 3: Get the Kuwaiti assemblies from the NCBI Pathogen Detection Isolates Browser

1. Search the Isolates Browser for BioProject PRJNA380997
   • https://www.ncbi.nlm.nih.gov/pathogens/isolates/#PRJNA380997