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.

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

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.

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.

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.