vincenzopennone's repositories
amr
amr_finder
bactopia
A flexible pipeline for complete analysis of bacterial genomes
BIGSdb
Bacterial Isolate Genome Sequence Database (BIGSdb): A platform for gene-by-gene bacterial population annotation and analysis.
bioconda-recipes
Conda recipes for the bioconda channel.
catalogue-browser
Source code of the catalogue browser java application.
cgview_comparison_tool
The CGView Comparison Tool (CCT) is a package for visually comparing bacterial, plasmid, chloroplast, and mitochondrial sequences.
drep
Rapid comparison and dereplication of genomes
Ellipsis
Plasmid assembly, gene identification and annotation pipeline
FastQC
A quality control analysis tool for high throughput sequencing data
galaxy-tools
A collection of bioinformatics tools for use with galaxy written at Quadram Institute
kaiju
Fast taxonomic classification of metagenomic sequencing reads using a protein reference database
LisSero
In silico serotype prediction for Listeria monocytogenes
MGEfams
Fast and robust identificaiton of mobile genetic elements (MGE) genes from genomes and metagenome assemblies using MGEfams, a high-quality and manually cruated subdatabase of profile hidden Markov models for MGE genes
MGERT
Mobile Genetic Elements Retrieving Tool
mob-suite
MOB-suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies
mobilome_2022
we examine the incidence and protein-protein interactions of all known plasmid-linked genes (n=9,172) across representative specimens from all bacteria (n=4,419).
phigaro
Phigaro is a scalable command-line tool for predicting phages and prophages
pima
Plasmid and antimicrobial resistance pipeline
PlasFlow
Software for prediction of plasmid sequences in metagenomic assemblies
plasmidID
PlasmidID is a mapping-based, assembly-assisted plasmid identification tool that analyzes and gives graphic solution for plasmid identification.
platon
Identification & characterization of bacterial plasmid-borne contigs from short-read draft assemblies.
rawgraphs-charts
A curated selection of charts provided through RAWGraphs interface
read2tree
a tool for inferring species tree from sequencing reads
Reads2Resistome
Hybrid and non-hybrid whole genome assembler with resistome identification for Illumina, PacBio and Nanopore reads.
rgi
Resistance Gene Identifier (RGI). Software to predict resistomes from protein or nucleotide data, including metagenomics data, based on homology and SNP models.
rMAP
Bacterial analysis Toolbox for profiling the Resistome of ESKAPE pathogens using WGS
SqueezeMeta
A complete pipeline for metagenomic analysis
staphopia-sccmec
A standalone version of Staphopia's SCCmec typing method.
sunbeam
A robust, extensible metagenomics pipeline