Projects in Awesome Lists by linsalrob

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

Last synced: 23 Mar 2025

https://github.com/linsalrob/sra_metadata

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

Last synced: 21 Jun 2025

https://github.com/linsalrob/sphae

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

Last synced: 23 Mar 2025

https://github.com/linsalrob/pyfba

A python implementation of flux balance analysis to model microbial metabolism

Last synced: 23 Mar 2025

https://github.com/linsalrob/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.

bioinformatics metagenomes metagenomic-data metagenomics sra

Last synced: 23 Mar 2025

https://github.com/linsalrob/prophagepredictioncomparisons

Comparisons of multiple different prophage predictions

Last synced: 23 Mar 2025

https://github.com/linsalrob/crassphage

Sequencing and analysis of crAssphage regions from around the globe

Last synced: 23 Mar 2025

https://github.com/linsalrob/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

bioinformatics phage

Last synced: 06 Nov 2025

https://github.com/linsalrob/genbank_to

Convert genbank files to a swath of other formats

Last synced: 27 Jul 2025

https://github.com/linsalrob/primer-trimming

Fast C code for identifying and removing primers and adapters

bioinformatics dna-sequences dna-sequencing

Last synced: 02 Apr 2026

https://github.com/linsalrob/fasta_validator

C code to validate a fasta file

Last synced: 02 Aug 2025

https://github.com/linsalrob/py_fasta_validator

A Python extension of the fasta validator

Last synced: 23 Mar 2025

https://github.com/linsalrob/phageproteomictree

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

awesomeness bioinformatics evolution evolutionary-algorithms phage phylogenetic-trees phylogenetics taxonomy

Last synced: 19 Jun 2025

https://github.com/linsalrob/phispyanalysis

Analysis of phispy data

Last synced: 08 Sep 2025

https://github.com/linsalrob/searchsratoolkit

Tools for processing data generated by the Search SRA

Last synced: 23 Mar 2025

https://github.com/linsalrob/cameragui

A repository for the Prosilica Camera GUI

Last synced: 21 Jul 2025

https://github.com/linsalrob/pyctv

Parse and incorporate the ICTV Virus Metadata Resource file

Last synced: 02 Feb 2026

https://github.com/linsalrob/repeatfinder

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

Last synced: 23 Mar 2025

https://github.com/linsalrob/searchsra

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

Last synced: 23 Mar 2025

https://github.com/linsalrob/atavide

Atavistic processing of metagenomics data.

bioinformatics bioinformatics-pipeline metagenomics metagenomics-binning metagenomics-counts metagenomics-toolkit

Last synced: 02 Aug 2025

https://github.com/linsalrob/coralimageanalysis

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

Last synced: 23 Mar 2025

https://github.com/linsalrob/genetic_codes

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

Last synced: 23 Mar 2025

https://github.com/linsalrob/mgi-adapters

Trim adapters from MGI sequence data

Last synced: 23 Mar 2025

https://github.com/linsalrob/qudaich

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

Last synced: 10 Sep 2025

https://github.com/linsalrob/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

Last synced: 23 Mar 2025

https://github.com/linsalrob/pppf

Probabilistic Phage Protein Functions

Last synced: 05 May 2026

https://github.com/linsalrob/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

Last synced: 02 Jul 2026

https://github.com/linsalrob/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

Last synced: 23 Mar 2025

https://github.com/linsalrob/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)

Last synced: 23 Mar 2025

https://github.com/linsalrob/seqc

C and C++ libraries for working with sequences

Last synced: 04 Jan 2026

https://github.com/linsalrob/pbj_placer

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

Last synced: 23 Mar 2025

https://github.com/linsalrob/commonworkflowlanguage

CWL codes and examples for searchSRA.org

Last synced: 23 Mar 2025

https://github.com/linsalrob/phispyweb

Running phispy, but on the web

Last synced: 26 May 2026

https://github.com/linsalrob/sra-cloud

Tools, tricks, tips, and uses for SRA in the cloud

google-cloud google-cloud-datastore ncbi sra

Last synced: 23 Mar 2025

https://github.com/linsalrob/sam

Working with Sam and Bam files using HTSLIBS

Last synced: 23 Mar 2025

https://github.com/linsalrob/phcirc

Phage genome recircularization

Last synced: 23 Mar 2025

https://github.com/linsalrob/reducedbacterialproteinsdatabase

A database of a reduced set of bacterial (and perhaps archaeal) proteins

Last synced: 02 May 2026

https://github.com/linsalrob/qiime_scripts

A few scripts that Rob has written to handle qiime files

Last synced: 23 Mar 2025

https://github.com/linsalrob/partie_hat

High throughput automated typing for the partition engine

Last synced: 08 Jul 2025

https://github.com/linsalrob/edwardslab-android

Automatically exported from code.google.com/p/edwardslab-android

Last synced: 23 Mar 2025

https://github.com/linsalrob/jetstream-sra-cluster-setup

This module sets up an autoscaled Jetstream cluster for SRA work, based on HTCondor, the OpenStack Shade library, and SaltStack.

Last synced: 04 May 2026

https://github.com/linsalrob/edwards-opensocial

Automatically exported from code.google.com/p/edwards-opensocial

Last synced: 23 Mar 2025

https://github.com/linsalrob/depth-profile-video-processing

Video processing tools for analyzing the depth profiles from Line Islands (and other coral reefs?) transects

Last synced: 23 Mar 2025

https://github.com/linsalrob/ceeqlib

Ceeqlib (pronounced seq-lib) is a library written in C for manipulating fastq and fasta files.

Last synced: 23 Mar 2025

https://github.com/linsalrob/seed_servers_python

Pythonic servers to access the SEED servers

Last synced: 22 Jun 2026

https://github.com/linsalrob/atlassensors

Last synced: 02 May 2026

https://github.com/linsalrob/bioinformatics

Robs General Bioinformatics Repo.... Free code for all to use

Last synced: 23 Mar 2025

https://github.com/linsalrob/augur

An augur was a priest and official in the classical Roman world. His main role was the practice of augury: Interpreting the will of the gods by studying the flight of birds – whether they were flying in groups or alone, what noises they made as they flew, direction of flight, and what kind of birds they were

Last synced: 08 Feb 2026