linsalrob

atavide

Atavistic processing of metagenomics data.

ComputationalGenomicsManual

Robs manual for the computational genomics and bioinformatics class.

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

fastq-pair

Match up paired end fastq files quickly and efficiently.

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.

PhiSpy

Prediction of prophages from bacterial genomes

PhispyAnalysis

Analysis of phispy data

PyFBA

A python implementation of flux balance analysis to model microbial metabolism

sphae

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

SRA_Metadata

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

linsalrob/crAssphage

Sequencing and analysis of crAssphage regions from around the globe

linsalrob/CommonWorkflowLanguage

CWL codes and examples for searchSRA.org

linsalrob/ete

Python package for building, comparing, annotating, manipulating and visualising trees. It provides a comprehensive API and a collection of command line tools, including utilities to work with the NCBI taxonomy tree.

linsalrob/pbj_placer

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

linsalrob/PhATE-1

Pipeline code for phage gene calling and annotation

linsalrob/UCCD

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

linsalrob/ADAPT

ADAPT presents a web-based system for the analysis of ARISA data sets

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

linsalrob/BAM_Scripts

Tools for (1) retrieving data from the Sequence Read Archive, (2) using Read Mapping for analysis, and (3) performing many common tasks when working with BAM/SAM files.

linsalrob/CAT

CAT/BAT: tool for taxonomic classification of contigs and metagenome-assembled genomes (MAGs)

linsalrob/ceeqlib

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

linsalrob/Computing-Metagenomes-In-The-SRA

A repository of code and examples that are associated with computing against metagenomes in the SRA

linsalrob/CONCOCT

Clustering cONtigs with COverage and ComposiTion

linsalrob/crAssphage_papers

A list of papers and publications related to crAssphage

linsalrob/EDirectCookbook

linsalrob/fastDemux

A program to demultiplex fastq files

linsalrob/Genotype-Phenotype-Modeling

Modeling growth of bacterial genomes and connecting genotype to phenotype

linsalrob/gretel-test

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.

linsalrob/multiPhATE

Throughput PhATE processing of draft or finished phage genomes

linsalrob/partie_hat

High throughput automated typing for the partition engine

linsalrob/ReducedBacterialProteinsDatabase

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

linsalrob/sam

Working with Sam and Bam files using HTSLIBS

linsalrob/SAM_Reader

A Python class for analyzing many BAM/SAM files.

linsalrob/SEED_Servers_Python

Pythonic servers to access the SEED servers

linsalrob/shovill

⚡♠️ Assemble bacterial isolate genomes from Illumina paired-end reads

linsalrob/snakemake

This is the development home of the workflow management system Snakemake. For general information, see

linsalrob/Snoopy

Code for sailing ... mostly manipulating weather and routing

linsalrob/squeakr

Squeakr: An Exact and Approximate k -mer Counting System

linsalrob/sra-cloud

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