CyVerse UK

Documentation

Wiki of CyVerseUK project. Tutorials and overview of technologies.

renseq

Renseq Pacbio pipeline

polymarker

Dockerized Agave app for Polymarker, a SNP assay development pipeline

templates

base templates for Dockerfile and wrappers

ansible_plays

blast

blast docker image and cyverse integration

cyverse_website

cyverseuk-util

A collection of scripts for the cyverse UK clusters

GWASSER

Dockerized Agave app for GWASSER, an R script for simple gwassing.

mikado

Docker image and JSON files for CyverseUK for Mikado, a lightweight Python3 pipeline to identify the most useful or “best” set of transcripts from multiple transcript assemblies

bedtools

Bowtie2

btrim

concatenate_files

Cufflinks

cut_columns

cutadapt

cyverseone

OpenNebula web api to instantiate services from CyVerse UK infrastructure

emblebi-ena-submit

Docker build to submit to the EMBL-EBI ENA

kallisto

MUSCLE

NCBI_SRA_import

ocsi

ontologizer

Retrieve_BIP_Phenotypes

Docker container for retrieveing Phenotypic data from the Brassica Information Portal. It uses the BIP-API, stores output in .csv-format and passes the Sequence IDs on into a .txt file for further queries.

samtools

sickle

Tophat2

Trimmomatic

docker image and Agave app for Trimmomatic software

uncompress_gunzip