Companion repository to the article: "Comparative whole-genome approach to identify bacterial traits for microbial interactions"

A containerized nextflow pipeline designed to annotate prokaryote genomes.

Empirical intron annotation for Loxodes magnus genome assembly

Scripts I wrote as a graduate research assistant while working on the Wyeomyia smithii Genome project for Dr. Elizabeth Cooper's Lab at UNC Charlotte

Viral genome assemble and characterisation

There is no function to fetch automatically the information on the reported pubmed articles links in the tair to be used for the language models, so i coded this function which will take the tair information, a gene or locus tag and will fetch the corresponding pubmed and then from the pubmed the corresponding abstracts

A genome annotation length calculator written in ruby. It invokes the shell subprocess with in ruby to parse the iterators at the faster rate. if you have dozens of genome sequenced, simply mention the column number and the iterator will hash the length. added support for the features as

Arche: a functional-optimized annotator for microbial meta(genomes)

Scripts and notes related to the manuscript: Stuart KC & Edwards RJ et al. 2022. Transcript- and annotation-guided genome assembly of the European starling. Molecular Ecology Resources, doi.org/10.1101/2021.04.07.438753. † joint first author

BED-to-GFF3 converter that runs in parallel

this function takes ids file with the gene of interest and the phytozome gff files and will fetch the pacid for the genes of interest.

a ruby gem for the parsing and extraction of the miniprot alignments to extract locus specific, ids specific, and score and iters

Linked Data Platform for Animal Breeding & Genomics

Backup an apollo instance to a git repository

Aphrocallistes vastus genome

A comparative annotation toolkit (CAT) pipeline for 304 fly genomes.

BLAST DataBase Manager

Ergatis is a web-based utility that is used to create, run, and monitor reusable computational analysis pipelines; I was a developer on this project at The Institute for Genomic Research/J. Craig Venter Institute from 2005 to 2008.

Human Genome-Wide Association Studies Data