Mick Watson

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

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

EG_MinION_2016. Edinburgh Genomics MinION training 2016

perceptions. Base R version of https://github.com/zonination/perceptions

poRe_docs.

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

PoreCamp. Markdown bioinformatics training materials for PoreCamp

nanopore-software. A list of software for Oxford Nanopore data

c_fast5. C code to extract data from fast5 files

viRome_legacy. Legacy R code for the R package viRome DOI:10.1093/bioinformatics/btt297

ZiBRA_Zika_Analysis. Analysis of public Zika data from the ZiBRA project

metagenomics_scripts. Python

RNAfreak. Scripts and data to make you freak out about RNA-Seq

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

poRe_scripts. Linux command line scripts to be used with poRe

MinION_SynthMetagenome. R

meta4. Simple DB schema for metagenomics

genedateR. R code to detect gene names converted to dates in R

DRAM_hacks. Hacks to get the DRAM sqlite DB to build

genome_vs_rh_maps. Preliminary code to plot genomic co-ords vs RH maps

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

bioinformatics_project. An empty bioinformatics project

westminster_voting_intention. Plot of Westminster voting intention polls

viRome. Code for viRome

snakemake_split. An example of splitting up Snakemake input into chunks using CheckM as an example

Ensembl_GTF_FASTA_test. Hacky scripts to compare Ensembl GTF to FASTA files

bcbio_ensembl_GRCh38_bundle. Munging Ensembl GRCh38 genome and annotation files for use in bcbio

cwl_rna_seq. A very basic CWL RNA-Seq workflow using Kallisto