mw55309/poRe_scripts

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Created about 9 years ago
Updated over 7 years ago

mw55309/poRe_scripts

mw55309

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Linux command line scripts to be used with poRe

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

ZiBRA_Zika_Analysis

Analysis of public Zika data from the ZiBRA project

metagenomics_scripts

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

MinION_SynthMetagenome

viRome_legacy

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

meta4

Simple DB schema for metagenomics

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

DRAM_hacks

Hacks to get the DRAM sqlite DB to build

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

bioinformatics_project

An empty bioinformatics project

excel_vs_multi_plot

Example of an Excel vs alternate plot, both in R

crisp_colours

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

kegg_diamond

Snakemake pipeline for converting FASTQ to KO counts using DIAMOND

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

Common Workflow Language

westminster_voting_intention

Plot of Westminster voting intention polls

viRome

Code for viRome