CyVerse UK

Mikado is a pipeline to identify the “best” set of transcripts from multiple transcript assemblies.

Same as `cyversewarwick/ocsi` with condor adaptemnts

Pipeline for SNP assays development to generate homoeologue-specific assays for polyploid species.

A simple program for simple GWAS-ing.

docker image for sickle to use in cyverseuk infrastructure

Cufflinks docker image for use in Cyverse UK infrastructure

MUSCLE docker image for use in cyverseuk infrastructure

trimmomatic docker image for cyverseuk infrastructure

samtools docker image

btrim docker image

ontologixer docker image v 2.1

cutadapt docker image

Tophat2 docker image for use in CyVerseUK applications

Docker image for Bowtie2 to be used in CyVerseUK application

NCBI SRA import tool

For retrieving phenotypic data & sequence identifiers from the Brassica Information Portal.

Balst Docker image

bedtools docker image

A Dockerfile for an Ubuntu image with fastq-dump

MrBayes w/ MPI

Beast2 package Agave app

portcullis tool by Dan Mapleson - https://github.com/maplesond/portcullis

Docker image for beast with beagle

RAxML agave docker app

RenSeq PACBio pipeline

Tuxedo suite pipeline for RNA-Seq analysis

Same as Polymarker, it provides the wheat genome.

A Docker image for kallisto.

test blast app