A strobemer-Based Profile Hidden Markov Model (sPHMM) approach to Taxonomic Identification of DNA Barcode Data.

To run this pipeline, the following files are needed in the same working directory in R/RStudio (R version 4.4.1 or higher):

• sPHMM_Pipeline_Train&CV.R
• sPHMM_Functions.R
• strobemer_extract.cpp
• strobemer_chop.cpp
• strobemer_extract.h
• strobemer_filter.cpp
• strobemer_filter_unique.cpp

HMMER3 must also be installed prior to using this pipeline (v 3.3.2 or higher)

Working directory must also include a folder containing the fasta files to be run on this pipeline ex: seqData/

A small barcode dataset (Branchiopoda) from BOLD (https://boldsystems.org/) has been added to run tests with the pipeline.

Functions get loaded from a separate R script and must be loaded before the analysis proceeds

source("sPHMM_Functions.R")

GPL-Licensed Code Attribution

The following files were renamed from the original repository:

• strobemer_extract.h (formerly strobemer.h, unmodified)
• strobemer_extract.cpp (formerly strobemer.cpp, unmodified)

Original repo: https://github.com/BGI-Qingdao/strobemer_cpptest

License: GPLv3