🦠📇 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.

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

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=".