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bbsrc_success

bcbio_ensembl_grch38_bundle

Munging Ensembl GRCh38 genome and annotation files for use in bcbio

bioinformatics_project

An empty bioinformatics project

c_fast5

C code to extract data from fast5 files

chicken_mag_mapping

coda_microbiome_tutorial

Workshop for NGS'18 conference, Barcelona 2018

crash_gcp

crisp_colours

Also known as chips in strange countries. A global standard for crisp/chip packaging colours.

cwl_rna_seq

A very basic CWL RNA-Seq workflow using Kallisto

demo

Demo repo for tutotial articles on Opensource.com

dog_microbiome

download_geba

Perl script to download the 1003 GEBA genomes doi:10.1038/nbt.3886

dram_hacks

Hacks to get the DRAM sqlite DB to build

eg_minion_2016

Edinburgh Genomics MinION training 2016

ensembl_gtf_fasta_test

Hacky scripts to compare Ensembl GTF to FASTA files

eu_referendum_polls

R plot of EU referendum polls

excel_vs_multi_plot

Example of an Excel vs alternate plot, both in R

festivalofgenomics

Demo for the London Festival of Genomics

fragilis_paper

Scripts in support of our B fragilis paper

genedater

R code to detect gene names converted to dates in R

genome_vs_rh_maps

Preliminary code to plot genomic co-ords vs RH maps

ideel

Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes

kegg_diamond

Snakemake pipeline for converting FASTQ to KO counts using DIAMOND

kraken_db_install_scripts

Updated Kraken DB install scripts to cope with new-ish NCBI structure

kraken_output_parser

Quick script to allow parsing of Kraken report files into nice manageable CSVs

lct_scripts

Scripts for lowest common taxon analysis

magcloudcosts

Costing MAG creation on the cloud

magpy

Snakemake pipeline for annotating metagenome-assembled genomes (MAGs) (pronounced mag-pie)

marc_code

My github to store random bits of code for MARC

meta4

Simple DB schema for metagenomics