🦠📇 Microbial genomes-to-report pipeline

UPHL's Reference Free Pipeline

Assembly and annotation of metatranscriptomic or metagenomic data for prokaryotic, eukaryotic and viruses.

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, …

The International Code of Nomenclature of Prokaryotes Described from Sequence Data

examination of genome size across all kingdoms

panicmage can estimate gene gain and loss rates, the size of pan-genomes, and test for neutral evolution.

Modelling evolution of genome size in prokaryotes in response to changes in their abiotic environment

A tool for dynamically calculating the codon usage bias in bacterial genomes and querying of a database for Codon Bias statistical analysis

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.

Repository hosting code and manuscript materials for DISA project at IITD

Variant Calling with Deep Learning for Prokaryotic genomes using TensorFlow. Adds (0 <= P(Variant) <= 1) to VCF files under INFO as abbreviated "ACC=".

Sup. Table 1 from Rodríguez-Gijón and Nuy et al., 2022 (Front. in Microbiology)