Training: Command Line

In silico serotyping

Install SeroBA (Epping et al 2018) as per instructions at https://github.com/sanger-pathogens/seroba#installation and git clone the database from the following link https://github.com/sanger-pathogens/seroba.git.

Files required to run serotyping using SeroBA:

  1. paired-end fastq files
  2. database
  3. sample list (only for running on multiple samples)

Run in silico serotyping on a single sample: 

serotype runSerotyping <full path to the database> <read 1> <read 2> <output folder prefix>

Run in silico serotyping on multiple samples:

  1. create a list of sample names and save it as samplelist (e.g. the sample name for 24371_8#283_1.fastq.gz is 24371_8#283) 
  2. for f in $(cat samplelist); do seroba runSerotyping <path to the database> ${f}_1.fastq.gz ${f}_2.fastq.gz ${f}; done
  3. seroba summary ./

Output:
summary.tsv

These instructions are available to download here:
Download

GPSC assignment

Install PopPUNK 2.4 as per instructions at PopPUNK documentation and download the GPS reference database and the GPS designation.

GPS reference database (n=42,163):
Download

GPS designation (933 GPSCs):
Download

Files required to run GPSC assignment using PopPUNK 2.4:

  1. A 2-column tab-delimited file containing sample name and path to the corresponding assembly (no header)
  2. GPS reference database <GPS_v6>
  3. GPS designation <GPS_v6_external_clusters.csv>

output directory name is assigned using --output
number of threads can be changed using –threads

Run GPSC assignment:

poppunk_assign --db GPS_v6 --distances GPS_v6/GPS_v6.dists --query <2-column path to assembly> --output <GPSC_assignment> --external-clustering GPS_v6_external_clusters.csv

Outputs:
_clusters.csv: popPUNK clusters with dataset specific nomenclature
_external_clusters.csv: GPSC v6 scheme designations

Novel Clusters are assigned NA in the _external_clusters.csv as they have not been defined in the v6 dataset used to designate the GPSCs. Please email: globalpneumoseq@gmail.com to have novel clusters added to the database and a GPSC cluster name assigned after you have checked for low level contamination which may contribute to biased accessory distances.

Merged clusters: Unsampled diversity may represent missing variation linking two clusters. GPSCs are then merged. For example if GPSC23 and GPSC362 merged, the GPSC would be then reported as GPSC23, with a merge history of GPSC23;362.

The instructions for PopPUNK v2.4 are available to download
Download

The instructions for PopPUNK v1 are available to download
Download