🦠📇 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, …
examination of genome size across all kingdoms
The International Code of Nomenclature of Prokaryotes Described from Sequence Data
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)
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