Bacterial swiss-army-knife pipeline for NGS data

Condense and summarize many results form PADLOC into CSV for heatmaps

PhyloTrace is a GUI platform for a fully controllable cgMLST analysis workflow.

A flexible pipeline for complete analysis of bacterial genomes

A faster implementation of the string search for the check of the insertion elements and the CRISPR sites if present in the genome string and then clip those insertion sites and get a clean genome.

a workflow for complete analysis of bacterial metagenomes and pagenome graphs and direct viewing in panchae. It will also analyze metagenomes from both illumina and long reads

a function to calculate the genome annotation for the microbiome and also for the other genomes. It will take a genome annotation or a text file and will prepare the count and also for the gene ontology analysis

python code which i coded using the mathematical expression for the genome based ontologies annotation and the phylogenomics informativeness

A keras implementation of machine learning for bacterial genomes, takes a fasta file and the annotation features and the genes you want to train the keras model

shell assembler that takes only the directory path and does all the cleaning of the reads, mapping, remapping and assembly. From start to finish everything by providing a simple directory path.

This repository contains a datascience based faster implementation of the domain predictions from the interpro scan and it will give you a complete domains information, coordinates and other associative information. I used a mapping dataframe approach to make it faster rather than looping it over and over.

a scalable and faster implementation for the genome and the transcriptome annotations for large scale sequencing datasets.

A R function for the analysis of the evolutionary rates from the fasta files, and uses the ka/ks and the dn/ds and plots the evolutionary rates.

Bioinformatics tool to find integrons in bacterial genomes

A Snakemake workflow assembling bacterial genomes according to the standard operating procedure in the Clavel Lab

The CGView Comparison Tool (CCT) is a package for visually comparing bacterial, plasmid, chloroplast, and mitochondrial sequences.

⚡ ♒ Rapid prokaryotic genome annotation

High-resolution strain-level microbiome composition analysis tool based on reference genomes and k-mers

An atlas of high-quality Bacillus cereus group genomes with standardized, manually curated metadata

Simple bacterial assembly and annotation pipeline