bacterial

FlowCraft: a component-based pipeline composer for omics analysis using Nextflow. 🐳📦

A mapping-based pipeline for creating a phylogeny from bacterial whole genome sequences

finding conserved regions in highly diverse genomes

Inofficial R client for the DSMZ's Bacterial Diversity Metadatabase (former contact: @katrinleinweber). https://api.bacdive.dsmz.de/client_examples seems to be the official alternatives.

The BV-BRC Web Application

bacQC is a bioinformatics analysis pipeline for assessing the quality of bacterial isolate sequence data

An R/Shiny Package for Bacterial TSS extraction, using Cappable-seq

Condense and summarize many results form PADLOC into CSV for heatmaps

Learn antimicrobial susceptibility testing techniques and how whole-genome sequencing and bioinformatics can be used to understand AMR

Computer vision in the service of bacteriology refers to the use of computer algorithms and technology to analyze and interpret images of bacteria for the purpose of identifying and characterizing different types of bacteria.

BioInfo Tools

code used in van Raaphorst, Kjos & Veening (2017), Chromosome segregation drives division site selection in Streptococcus pneumoniae, PNAS

Bacterial gene duplication analysis pipeline

Implementation and explanation of the Bacterial Foraging Optimization (BFO) algorithm, with examples and visualization, suitable for AI and optimization studies.

Bacterial ASsembly contaminaTION

PLAKAT — Precised Local Alignment marKers Analysis Tool — is a genome-guided workflow for discovering short, species-specific DNA marker regions from bacterial genomes.

Variant barcoding pipeline using single nucleotide polymorphisms (SNPs) for the generation of M. orygis standardised markers for diagnostic and epidemiological use.

Docker-based implementation of the Discover1.1 pipeline for bacterial characterization.

Docker-based implementation of the Discover1.1 pipeline for bacterial characterization.

Curve Growth modeling-IPASS project