Stars
A novel improved pipeline for riboswitch classification based on SMOTE etc.
Plasmid analysis using rearrangement distances
A tool for generating consensus long-read assemblies for bacterial genomes
Searching large collections of sequencing data with genome-scale queries
A toolbox for pangenome analysis and threshold evaluation.
Source code for my dissertation on the phylogeography of Xanthomonas campestris pv. campestris.
All project scripts and docs related to the TNAU genomics aspect of my thesis (Chapter 2)
Official home of genome aligner based upon notion of Cactus graphs
Lima - Demultiplex Barcoded PacBio Samples
This RAPT repository has been retired as of December 2024. NCBI's Read assembly and Annotation Pipeline Tool (RAPT) was a pilot service.
REference Sequence annotation and CuRatIon Pipeline
Code for design of diagnostic PCR primers, and metabarcoding markers.
Deep networks for protein functional inference
This package contains Perl programs/scripts that perform frequently needed operations on FASTA format files.
BRIG is a cross-platform (Windows/Mac/Unix) application that can display circular comparisons between a large number of genomes, with a focus on handling genome assembly data.
Python library to facilitate genome assembly, annotation, and comparative genomics
Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes
Foreign Contamination Screening caller scripts and documentation
Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes