prokka

Insertion sequences (Insertion Element) [https://en.wikipedia.org/wiki/Insertion_sequence] collected from ISfinder (https://isfinder.biotoul.fr/)

Analyzing the genomic and metagenomic features of SGB748 MAGs from oral samples to uncover their role in health and peri-implant diseases through patient metadata integration.

Prokka批量执行脚本 Batch Prokka can help you execute prokka batch assemblies.

Genome assembly annotation of Lactiplantibacillus plantarum from Illumina NGS data using Prokka v1.15.6 following de novo assembly with SPAdes.

Plasmidome analysis to track the transfer route of AMR genes in bacteria

A script for downloading complete sequences from genbank and make blast database for use with prokka

🦇🧫📊Study on bat gut shotgun metagenomics

End-to-end automated bioinformatics pipeline for bacterial genome assembly and functional annotation (SRR35523993).

A tool to take annotation files from bakta or prokka and produce a human readable report.

Bakta and Prokka call the same 87,859 CDS regions in 25 complete bacterial genomes, then give 51.7% of them different product names. Both wrap Prodigal, so they agree on gene boundaries and diverge on function. Grouped-by-genome ML shows the disagreement tracks database coverage, not sequence.

Bio-Gen: An automated, containerized pipeline for bacterial genome assembly and annotation. Built on Ubuntu 24.04, it integrates fastp, SPAdes, Pilon, and Prokka to transform raw reads into polished GenBank files and MultiQC reports with a single command.

Nextflow DSL2 pipeline for bacterial whole-genome assembly from Oxford Nanopore reads: Flye assembly, Medaka polishing, Prokka annotation, CheckM QC, and AMRFinderPlus AMR detection. Containerized.

[a.a. 23/24] M. Gambardella

Graph-based pangenomic and synteny analysis of Helicobacter pylori (n=41 complete RefSeq genomes) using PPanGGOLiN, with reproducible workflows for annotation (Prokka), ANI quality control (FastANI), core-genome phylogeny (MAFFT + IQ-TREE 2), resistome profiling (AMRFinderPlus), and publication-grade visualizations.

Minimal pixi proof-of-concept for biologists — Prokka, Bakta and Snakemake in four isolated environments

Montagem de genoma bacteriano: Trimmomatic, SPAdes, QUAST, Prokka, BLAST

This project is part of the course of Computational Microbial Genomics, held by Nicola Segata (A.Y. 2021-2022) @ University of Trento.

Projeto elaborado para WBDS LA CAMP- Anotação do genoma da bactéria Clostridium botulinum com pyrodigal e prokka

Reproducible figure pipeline for the draft genome of lactic acid bacterium isolate S1A: a circular genome map, a class II bacteriocin locus diagram, and predicted regulator families stratified by evidence tier. Genomic figure contribution to a study of LAB-loaded cellulose hydrogels. Predicted gene content, not measured activity.

Reusable bacterial genome analysis pipeline for paired-end FASTQ data using FastQC, fastp, SPAdes, QUAST, Prokka, and MultiQC.