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Organization:
CDC/NCEZID/DVBD

Contact:
Lynn M Osikowicz
vir5@cdc.gov

Overview

This bioinformatics pipeline identifies and summarizes amplicon sequences produced by the multiplex PCR amplicon sequencing (MPAS) described by Hojgaard et. al (2020). The MPAS assay was originally designed to detect microbial genera that contain known human pathogens found in Ixodes ticks (Borrelia spp. Babesia spp., Anaplasma spp. Ehrlichia spp.). This pipeline is implemented in Nextflow and performs QC analysis, primer trimming, error correction, alignment to reference sequences, NCBI BLAST of unaligned sequences, phylogenetic tree creation of aligned sequences, and report generation.

To run this pipeline, see pipeline instructions

This pipeline was developed by Mark Stenglein from Colorado State University in collaboration with Lynn Osikowicz, Sarah Maes, Andrias Hojgaard, and Becky Eisen from the CDC's Division of Vector-Borne Diseases.

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Pipeline References

Hojgaard, A., Osikowicz, L. M., Eisen, L., & Eisen, R. J. (2020). Evaluation of a novel multiplex PCR amplicon sequencing assay for detection of human pathogens in Ixodes ticks. Ticks and tick-borne diseases, 11(6), 101504. doi:10.1016/j.ttbdis.2020.101504. PMID: 32993925.

Osikowicz LM, Hojgaard A, Maes S, Eisen RJ, Stenglein MD. A bioinformatics pipeline for a tick pathogen surveillance multiplex amplicon sequencing assay. Ticks Tick Borne Dis. 2023 Sep;14(5):102207. doi: 10.1016/j.ttbdis.2023.102207. Epub 2023 May 27. PMID: 37247570.