Baargin
Baargin: a Nextflow workflow for the automatic analysis of bacterial genomics data with a focus on Antimicrobial Resistance - Published in JOSS (2023)
gtdbtk
GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.
cb-platon
Identification & characterization of bacterial plasmid-borne contigs from short-read draft assemblies.
https://github.com/bioatmosphere/microbiome-drought-legacy
A theorectical investigation into mechanisms of drought legacy formation and influencing factors in soil microbiomes using DEMENTpy.
bacqc
bacQC is a bioinformatics analysis pipeline for assessing the quality of bacterial isolate sequence data
assemblebac
avantonder/assembleBAC is a bioinformatics best-practise analysis pipeline for assembling and annotating bacterial genomes.
https://github.com/asadprodhan/bacterial-phylogenetic-tree-reconstruction-using-ubcg-pipeline
Identifying pathogenic bacteria
assemblebac-ont
avantonder/assembleBAC-ONT is a bioinformatics pipeline that de novo assembles and annotates Oxford Nanopore (ONT) long-read sequence data.
bacqc-ont
bacQC-ONT is a bioinformatics pipeline for the assessment of Oxford Nanopore sequence data
eggsurfacemicrobiome
Reproducible documentation for "Heussler and Klammsteiner et al. (2023). Microbial influences on black soldier fly reproduction: A focus on egg surface colonization. Research Square Preprint"
bacteria_analyzer
Interactive program for handling data related to growth rates of different bacteria at different temperatures.