rKOMICS

rKOMICS analyzes mitochondrial minicircle sequence diversity from kinetoplastid NGS datasets to characterize minicircle and maxicircle assemblies for studies of trypanosomatid mitochondrial genomes.

Key Features:

• KOMICS (Python package v3.7): automates assembly and circularization of mitochondrial genomes (maxicircles and minicircles) from NGS datasets.
• Input/output formats: processes sequencing reads in FASTQ format and outputs assembled maxicircle sequences and circularized minicircles in FASTA format.
• Minicircle diversity analysis (rKOMICS R package): generates minicircle sequence alignments and analyzes minicircle sequence clusters to summarize sequence diversity.
• Population-scale analysis: enables examination and summarization of minicircle sequence diversity across multiple samples simultaneously.
• Taxonomic scope: applicable to trypanosomatids within the Kinetoplastida, including representation across 27 genera.

Scientific Applications:

• Population diversity studies: comparison of minicircle sequence richness and composition among subspecies and subpopulations.
• Marker discovery: identification of species-specific molecular markers from minicircle sequence clusters.
• Evolutionary inference: investigation of the evolutionary history and structure of parasitic protozoa mitochondrial genomes.
• Empirical demonstration: applied to a whole-genome sequencing dataset of the Leishmania braziliensis species complex from Peru to reveal differences in minicircle richness and composition.

Methodology:

KOMICS assembles and circularizes mitochondrial genomes from NGS FASTQ reads to produce maxicircle and circularized minicircle FASTA sequences; rKOMICS generates minicircle sequence alignments, performs clustering of minicircles, and summarizes sequence diversity.