vincenzopennone's repositories
ARG-contig_mobilome_analysis
This pipeline performs a mobilome analyses on previously selected contigs, those harboring antimicrobial genes from ResFinder database, to confirm or discard the location of such genes within plasmid or chromosomal, or even within integron or lateral gene transfer (lgt) regions. It can be adapted to other purposes (databases), according to user requeriments.
ARG_bowtie_blast
This is a pipeline to screen antimicrobial resistance genes (ARGs) by a 2 step approach: fastq alignment to ResFinder database by bowtie2, plus an additional BLAST against the same database.
bioperl-live
Core BioPerl 1.x code
concat_cgMLST_genes
A ruby script to concatenate cgMLST genes obtained by fast-GeP (https://github.com/jizhang-nz/fast-GeP)
contig_taxonomy
This is a pipeline to make the contigs taxonomic assignment by kraken2, mmseqs2 and diamond approaches using the same database, and finally select the genus level classification if at least 2 of the approaches have the same result. In this case, we have worked with the kraken2-microbial database.
download_genomes
This pipeline was done to automatize the download of genomes and attached information (metadata) from PUBMLST, NCBI and PATRIC repositories.
efsa-catalogues
Repository used to store the .ecf catalogues.
galaxy
Data intensive science for everyone.
gwas_scripts
Codebook from my GWAS cookbook
Integron_Finder
Bioinformatics tool to find integrons in bacterial genomes
MetagenomicAntibioticResistance
NastyBugs: a simple method for extracting antimicrobial resistance information from metagenomes
MetaMaps
Long-read metagenomic analysis
mlst
:id: Scan contig files against PubMLST typing schemes
pavian
🌈 Interactive analysis of metagenomics data
perf
PERF is an Exhaustive Repeat Finder
Prodigal
Prodigal Gene Prediction Software
Roary
Rapid large-scale prokaryote pan genome analysis
Scoary
Pan-genome wide association studies
spaTyper
Computational method for finding spa types.
staramr
Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.
symmetrical-broccoli
First test repository
tormes
Making whole bacterial genome sequencing data analysis easy
treeWAS
treeWAS: A Phylogenetic Tree-Based Tool for Genome-Wide Association Studies in Microbes