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A Snakemake pipeline for Ralstonia solanacearum species complex (RSSC) sequevar typing based on the endoglucanase (egl) gene. The pipeline extracts the egl gene from bacterial genome assemblies via in-silico PCR, trims it to the ~698 nt phylogenetically informative region, aligns query sequences with curated reference sequevars, builds a maximum-likelihood phylogenetic tree, and produces an annotated tree visualization. Finally, it assigns a sequevar to each query genome based on the nearest reference in the tree. This workflow enables rapid and reproducible sequevar typing for RSSC genomes.

Adaptation of LNPR for carbon modelling:

includes scripts for transfer to carbon input includes uv to initiate R runs in jupyter lab

A comprehensive Snakemake workflow for assembling high-quality bacterial genomes from Oxford Nanopore long-read sequencing data. The pipeline integrates Autocycler consensus assembly with multiple assemblers (Canu, Flye, Plassembler), performs quality control with Filtlong and Porechop, applies Racon polishing, and provides comprehensive quality assessment using QUAST, BUSCO, and CheckM2. All steps are containerized with conda environments for reproducible results. They include automated HTML/PDF/TXT reporting.

This repository contains a Snakemake bacterial assembly QC pipeline to perform quality control. It will use Quast (metrics), CheckM2 (completedness and contamination), Busco (completedness), skANI (taxonomic assignment against GTDB with ANI). It will also produce a Busco plot summary, a beeswarm plot of N50 and number of contigs, and an excel file with Quast, CheckM2 and skANI summaries.

This repository contains a Snakemake workflow tailored for assembling bacterial genomes from long-read data generated with R10.4.1 simplex reads from Oxford Nanopore Technologies and includes several QC steps on the resulting assemblies.

Illumina bacterial assembly snakemake is a snakemake pipeline to assemble lots of bacterial genomes from Illumina paired-end short-reads (typically 150bp); It also performs several QC steps on the reads and on the resulting assemblies. Everything needed can be found in this repository (except for the GTDB reference database for taxonomic assembly classification and the Kraken2 database for taxonomical read classification).