linsalrob

Rob Edwards's repositories

ComputationalGenomicsManual

Robs manual for the computational genomics and bioinformatics class.

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fastq-pair

Match up paired end fastq files quickly and efficiently.

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PhiSpy

Prediction of prophages from bacterial genomes

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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

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sphae

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

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genbank_to

Convert genbank files to a swath of other formats

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primer-trimming

Fast C code for identifying and removing primers and adapters

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mgi-adapters

Trim adapters from MGI sequence data

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PhispyAnalysis

Analysis of phispy data

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repeatfinder

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

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alphafold

Open source code for AlphaFold.

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atavide

Atavistic processing of metagenomics data.

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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

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genetic_codes

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

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SUPER-FOCUS

A tool for agile functional analysis of shotgun metagenomic data

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acacia-stream

testing some streaming using minimap and acacia and something

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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)

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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

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