linsalrob/ProphagePredictionComparisons

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linsalrob/ProphagePredictionComparisons

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Comparisons of multiple different prophage predictions

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

Jupyter Notebook

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

Jupyter Notebook

SRA_Metadata

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

PyFBA

A python implementation of flux balance analysis to model microbial metabolism

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.

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 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

genbank_to

Convert genbank files to a swath of other formats

mgi-adapters

Trim adapters from MGI sequence data

primer-trimming

Fast C code for identifying and removing primers and adapters

fasta_validator

C code to validate a fasta file

py_fasta_validator

A Python extension of the fasta validator

PhispyAnalysis

Analysis of phispy data

Jupyter Notebook

PhageProteomicTree

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

pyctv

Parse and incorporate the ICTV Virus Metadata Resource file

cameraGUI

A repository for the Prosilica Camera GUI

repeatfinder

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

SearchSRA

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

SearchSRAToolKit

Tools for processing data generated by the Search SRA

atavide_lite

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

qudaich

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 University

genetic_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 sequences

CommonWorkflowLanguage

CWL codes and examples for searchSRA.org

Common Workflow Language

PPPF

Probabilistic Phage Protein Functions

UCCD

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

Jupyter Notebook

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

acacia-stream

testing some streaming using minimap and acacia and something

pbj_placer

Rewrite jplacer files from phylosift for importing into ITOL and other tree viewing software

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