LexicMap: efficient sequence alignment against millions of prokaryotic genomes
EzAAI - High Throughput Prokaryotic AAI Calculator
Query sequence database by HMMs arranged in predefined synteny structure
Tool intended to pull out sequences and annotations between insertion sites specified by the user.
WDL-based tool designed to streamline microbiome data processing for assembling, polishing, annotating, and visualizing prokaryotic genomes. It simplifies the analysis process from raw sequencing reads to high-quality annotated genomes
This project was written as a first step to apply the ddRADSeq genotyping method to prokaryota. This code is made to dertemine, in silico, the couple of enzymes to apply on a given sequence.
In this repository live the bash, R and Julia scripts used to explore the microdiversity of the prokaryotic community at Uranouchi Inlet (42-sample time-series) by means of metagenomic shotgun sequencing under the supervision of the Ogata Lab.
Python CLI tool & package. An LLM-guided Post-Annotation Synthesizer that turns complex prokaryotic genome annotations into human-readable summaries & machine-readable JSON.
In this repository live the bash, R and Julia scripts used to explore the microdiversity of the prokaryotic community at Uranouchi Inlet (9-sample time-series) by means of metagenomic shotgun sequencing under the supervision of the Ogata Lab.
Variant Calling with Deep Learning for Prokaryotic genomes using TensorFlow. Adds (0 <= P(Variant) <= 1) to VCF files under INFO as abbreviated "ACC=".
This repository contains a set of scripts and workflows designed to search for Respiratory Complex I (NADH Ubiquinone Oxidoreductase) subunits in prokaryotic genomes and proteomes.
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