In this repository we have some tools that we will use to distinguish the presence or absence of species in a metagenome made up of closely related species. In particular, we want to determine the presence of Clavibacter michiganensis michiganensis in a sample made up of various Clavibacter subspecies.
In this folder we find some scripts with examples of Topological Data Analysis (TDA) libraries and with the aim of applying them to the study of metagenomic and pangemomic data.
With this notebook, we use PyMetaSeem to generate random reads from various clavibacter michiganensis subspecies stored in /genomes/clavibacter/.
In this case, we can generate CSV files, with a Read to Organism Mapping (ROM) between the simulated metagenomes and the database using bowtie2.
In this script, we used the techniques of TDA was proposed by Aldo and eal. to identify the false positives in a group metagenomics data.
Clavibacter_michiganensis_subsp_capsici_1101.fna
Clavibacter_michiganensis_subsp_insidiosus_ATCC_10253.fna
Clavibacter_michiganensis_subsp_michi_contigs.fna
Clavibacter_michiganensis_subsp_nebraskensis_419B.fna
Clavibacter_michiganensis_subsp_sepedonicus_ATCC33113.fna
Clavibacter_michiganensis_subsp_tessellarius_ATCC_33566.fna
CP019409.fasta CP019417.fasta CP022135.fasta CP022494.fasta
CP019116.fasta CP019410.fasta CP019418.fasta CP022138.fasta CP022497.fasta
CP019403.fasta CP019411.fasta CP022015.fasta CP022139.fasta CP022500.fasta
CP019404.fasta CP019412.fasta CP022019.fasta CP022142.fasta CP022503.fasta
CP019405.fasta CP019413.fasta CP022034.fasta CP022467.fasta CP022504.fasta
CP019406.fasta CP019414.fasta CP022116.fasta CP022489.fasta
CP019407.fasta CP019415.fasta CP022117.fasta CP022490.fasta
CP019408.fasta CP019416.fasta CP022120.fasta CP022491.fasta