a computational pipeline for typing the Borrelia OspA protein
LISTT assigns in-silico types based on sequence of the OspA protein. Illumina NGS reads of a Borrelia isolate or its genome sequence can be provided as input. 25 in-silico types (ISTs) can currently be assigned, with ISTs 1-8 corresponding to the canonical OspA serotypes 1-8:
| Genospecies | OspA in-silico type |
|---|---|
| B. burgdorferi s.s. | 1 |
| B. afzelii | 2 |
| B. garinii | 3, 5, 6, 7, 8, 11, 12 |
| B. bavariensis | 4, 9, 10 |
| B. spielmanii | 13 |
| B. mayonii | 14 |
| B. valaisiana | 15, 25 |
| B. turdi | 16, 24 |
| B. yangtzensis | 17 |
| B. americana | 18 |
| B. bissettiae | 19 |
| B. carolinensis | 20 |
| B. finlandensis | 21 |
| B. japonica | 22 |
| B. lusitaniae | 23 |
The full method for IST assignment is described in the publication: https://pubmed.ncbi.nlm.nih.gov/38787376/
Clone the repository and enter the directory:
git clone https://github.com/Pfizer-opensource/LISTT.git
cd LISTT
Build and activate the environment:
conda env create -f environment.yml
conda activate ospa_ist
LISTT takes an assembled Borrelia genome or Illumina NGS reads of the ospA gene as input:
python ospa_typing.py -r1 [read1 fastq] -r2 [read2 fastq] -m r
python ospa_typing.py -g [genome fasta] -m a
Users may also specify the input file(s) location [-p] if an absolute path is not provided.
Analysis will fail if there is insufficient coverage of ospA or if ospA is truncated in the genome assembly.
Test genomes are sourced from the PubMLST genome sequence database
For more information, contact [email protected]