We use tools from different levels to compare Listeria Monocytogenes isolates.
This pipeline is specific for BIOL7210 group project. We have 6 tool avaliable which are listed below. Run on command line by choosing a tool. e.g., <./tool_functions FastANI> will only run FastANI, and output ANI scores.
Average Nucleotide Level, input fasta file, output ANI score.
7-gene-mlst, input fastq file, output mlst allele matrix.
Phylogeny level-cgMLST, input fasta file, output allele matrix, Genome Quality plot, results_statistics.tsv, results_contigsinfo.tsv.
Phylogeny level-SNP-based, input is a txt file with a list of paths to fasta files, output tipAlleleCounts maximum likelihood phylogentics tree.
Pan-genome analysis
Pan-genome analysis
The tools FastANI, StringMLST, ChewBBACA, kSNP, Roary, BPGA are installed using mini conda environment and manual installations in the server.
Miniconda environment for Linux 64-bit is set up in the server, with Python version 3.7. The tools installed in the T3env4 are : FastANI v1.3, Roary v3.13.0, Ete3 v3.1.1, r 3.6.0, ggplot2 v3.1.1, gnuplot v5.2.7. The T3env of miniconda has the tool kSNP v3.1.
Analysis of virulence and antibiotic resistance genes is done using gffconverter.py. The CARD and VFDB gff provided by functional annotation were used as input. This code generates a file with isolates and their associated virulence or antibiotic resistance genes information. A presence absence gene matrix for all isolates is also generted as output.
*This script uses -w flag with input for working directory where respective files with annotations are stored. -f flag is 1 if the files are just genes list from CARD and VFDB annotations, and is 0 when using merged GFF files are present in working directory.