Rob Edwards

ComputationalGenomicsManual. Robs manual for the computational genomics and bioinformatics class.

fastq-pair. Match up paired end fastq files quickly and efficiently.

PhiSpy. Prediction of prophages from bacterial genomes

SRA_Metadata. Get, parse, and extract information from the SRA metadata files

sphae. Phage annotations and predictions. A spae is a prediction or foretelling. We'll foretell you what your phage is doing!

EdwardsLab. Code from the Edwards lab, including bioinformatics, image analysis and more. All this code is created and maintained by folks at Rob Edwards' bioinformatics lab at Flinders University

genbank_to. Convert genbank files to a swath of other formats

PyFBA. A python implementation of flux balance analysis to model microbial metabolism

ProphagePredictionComparisons. Comparisons of multiple different prophage predictions

partie. PARTIE is a program to partition sequence read archive (SRA) metagenomics data into amplicon and shotgun data sets. The user-supplied annotations of the data sets can not be trusted, and so PARTIE allows automatic separation of the data.

crAssphage. Sequencing and analysis of crAssphage regions from around the globe

PhageHosts. This is the complete code base used in Robert A. Edwards, Katelyn McNair, Karoline Faust, Jeroen Raes, and Bas E. Dutilh (2015) Computational approaches to predict bacteriophage–host relationships. FEMS Microbiology Reviews doi: 10.1093/femsre/fuv048

fasta_validator. C code to validate a fasta file

mgi-adapters. Trim adapters from MGI sequence data

primer-trimming. Fast C code for identifying and removing primers and adapters

py_fasta_validator. A Python extension of the fasta validator

PhageProteomicTree. The phage proteomic tree was a breakthrough in evolution, taxonomy, and phylogenetics ... but nobody realized its global importance

SearchSRA. Tools to search through the Sequence Read Archive using XSEDE's Jetstream

repeatfinder. fast code for searching for direct and indirect repeats in DNA sequences.

atavide_lite. A simpler version of atavide that relies only on slurm or PBS scripts. Some of the settings are specific for our compute resources

pyctv. Parse and incorporate the ICTV Virus Metadata Resource file

PhispyAnalysis. Analysis of phispy data

SearchSRAToolKit. Tools for processing data generated by the Search SRA

cameraGUI. A repository for the Prosilica Camera GUI

get_orfs. C code to translate a DNA sequence using different translation tables. Designed to be fast and lightweight, with few dependencies (only zlib and pthreads)

genetic_codes. Python code for translating sequences using different NCBI translation tables and genetic codes.

PHROG_structures. View and download structures for representatives of all the PHROG data

CoralImageAnalysis. A central repo for all the coral image analysis code generated by the Edwards bioinformatics lab at San Diego State University

qudaich. Qudaich (queries and unique database alignment inferred by clustering homologs) is a software package for aligning sequences.

UCCD. Using Machine Language to Compare Ulcerative Colitis and Crohn's Disease

CF_Data_Analysis_Development. CF Data Analysis

PhiSigns. PhiSiGns is a web-based and standalone application that provides a simple and convenient tool to identify signature genes and design primers for PCR amplification of related genes from environmental samples

CommonWorkflowLanguage. CWL codes and examples for searchSRA.org

fast-adapter-trimming. Quickly remove adapters from DNA sequence files

pawsey. Code for running lots of different things on pawsey. This is a bit of a generic bucket and some of the code will be duplicated elsewhere in different projects