There are no reviews yet. Be the first to send feedback to the community and the maintainers!
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 genomesEdwardsLab
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 UniversitySRA_Metadata
Get, parse, and extract information from the SRA metadata filesPyFBA
A python implementation of flux balance analysis to model microbial metabolismProphagePredictionComparisons
Comparisons of multiple different prophage predictionspartie
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.sphae
Phage annotations and predictions. A spae is a prediction or foretelling. We'll foretell you what your phage is doing!crAssphage
Sequencing and analysis of crAssphage regions from around the globePhageHosts
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/fuv048genbank_to
Convert genbank files to a swath of other formatsmgi-adapters
Trim adapters from MGI sequence dataprimer-trimming
Fast C code for identifying and removing primers and adaptersfasta_validator
C code to validate a fasta filepy_fasta_validator
A Python extension of the fasta validatorPhispyAnalysis
Analysis of phispy dataPhageProteomicTree
The phage proteomic tree was a breakthrough in evolution, taxonomy, and phylogenetics ... but nobody realized its global importancepyctv
Parse and incorporate the ICTV Virus Metadata Resource filecameraGUI
A repository for the Prosilica Camera GUIrepeatfinder
fast code for searching for direct and indirect repeats in DNA sequences.SearchSRA
Tools to search through the Sequence Read Archive using XSEDE's JetstreamSearchSRAToolKit
Tools for processing data generated by the Search SRAatavide_lite
A simpler version of atavide that relies only on slurm or PBS scripts. Some of the settings maybe specific for our compute resourcesqudaich
Qudaich (queries and unique database alignment inferred by clustering homologs) is a software package for aligning sequences.atavide
Atavistic processing of metagenomics data.CoralImageAnalysis
A central repo for all the coral image analysis code generated by the Edwards bioinformatics lab at San Diego State Universitygenetic_codes
Python code for translating sequences using different NCBI translation tables and genetic codes.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)seqc
C and C++ libraries for working with sequencesCommonWorkflowLanguage
CWL codes and examples for searchSRA.orgPPPF
Probabilistic Phage Protein FunctionsUCCD
Using Machine Language to Compare Ulcerative Colitis and Crohn's Diseasepawsey
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 projectsacacia-stream
testing some streaming using minimap and acacia and somethingPhiSigns
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 samplesLove Open Source and this site? Check out how you can help us