⚡🦠🧬📇 Rapid microbial genomes-to-report pipeline
Assembly and annotation of metatranscriptomic or metagenomic data for prokaryotic, eukaryotic and viruses.
UPHL's Reference Free Pipeline
We present HRIBO (High-throughput annotation by Ribo-seq), a workflow to enable reproducible and high-throughput analysis of bacterial Ribo-seq data. The workflow performs all required pre-processing steps and quality control. Importantly, HRIBO outputs annotation-independent ORF predictions based on two complementary prokaryotic-focused tools, …
mash works best when given a mash dist file with a bunch of references.
The International Code of Nomenclature of Prokaryotes Described from Sequence Data
examination of genome size across all kingdoms
Tool for identifying the genetic translation table used by prokaryotic organisms
DeepCDS: Ab initio coding sequence prediction in prokaryotic short reads
Adaptive HGT-aware phylogenomic pipeline for prokaryotic marker gene selection and species tree inference
A tool for dynamically calculating the codon usage bias in bacterial genomes and querying of a database for Codon Bias statistical analysis
panicmage can estimate gene gain and loss rates, the size of pan-genomes, and test for neutral evolution.
Prokaryotic nomenclature assistant: deterministic, auditable decision support for naming prokaryotic taxa under the ICNP and the SeqCode
Command-line tool for retrieving pangenomes using the PanGBank API.
Sup. Table 1 from Rodríguez-Gijón and Nuy et al., 2022 (Front. in Microbiology)
Modelling evolution of genome size in prokaryotes in response to changes in their abiotic environment
🥔🐶 Species detection buddy
Pipeline for improving the Lotus japonicus genomes using an hybrid assembly approach
Prédiction auto-entraînée de gènes procaryotes (Python, Biopython) et évaluation rigoureuse face à l'annotation GenBank : CLI, rapport HTML, dashboard Streamlit.
Sequence processing and analysis code used to investigate the effects of different DNA extraction methods and PCR variability on multi-taxon DNA meta-barcoding estimates of soil biodiversity.
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