The Global Pneumococcal Sequencing (GPS) Project aims to strengthen worldwide genomic surveillance of Streptococcus pneumoniae through a decentralised data generation and analysis network to provide evidence for pneumococcal disease control. This GitHub organisation hosts open source tools, databases, and tutorials created under the GPS project.
| Repository | Purpose | |
|---|---|---|
| GPS Pipeline | GlobalPneumoSeq/gps-pipeline |
A Nextflow pipeline designed for processing raw reads (FASTQ files) of Streptococcus pneumoniae samples |
| SeroBA v2 | GlobalPneumoSeq/seroba |
A k-mer based pipeline to identify the serotype from Illumina NGS reads |
| CPS Extractor Pipeline | GlobalPneumoSeq/cps_extractor |
A Nextflow pipeline designed for processing Streptococcus pneumoniae reads to extract the capsular locus sequence (CPS) and check for disruptive mutations |
| Repository / Link | Purpose | |
|---|---|---|
| GPS Database | GPS Database Overview | Access point of all publicly available GPS data and its metadata |
| PopPUNK GPS Database | Database v10 (.zip or .tar.gz) GPSC designation v10 |
The latest PopPUNK database to assign Global Pneumococcal Sequence Cluster (GPSC) |
| GPSC Reference Genomes | GlobalPneumoSeq/gpsc-reference-genomes |
Assemblies ( .fasta ) and annotations ( .gff3) of reference genomes for 73 common GPSCs |
| Repository | Purpose | |
|---|---|---|
| FASTQ to Microreact | GlobalPneumoSeq/fastq-to-microreact |
A tutorial on how to go from raw read sequencing files (FASTQ) to a Microreact visualisation instance for Streptococcus pneumoniae |