Data and Metadata

1000 Genomes Mirror

RDS Genomics Collections Metadata Submission System

Tools

RDS Life Sciences (Genomics) Project Beacon Tutorial

Galaxy Queensland (genomic data processing and tutorials)

Training

Genomics Virtual Lab Blog (contains training materials)

Winter School in Mathematical & Computational Biology


Getting started with de novo assembly in Galaxy

This training material provides an overview of tools for de novo transcriptome assembly available on Galaxy-qld. It contains background on the theory of assembly as well as examples of tools usage through links to histories published on Galaxy-qld:

de novo transcript assembly with Trinity
Remove spaces from read names in FASTQ
Count reads with eXpress
Coverage for assembled transcripts
eXpress with sorted BWA-MEM alignment
Counting reads with the latest RSEM (February 2016)
Counting reads with Salmon

More Information


Public data on Galaxy-qld

This training material from Galaxy-qld users’ meeting describes public data available on Galaxy-qld server , such as built-in aligner indices and datasets available as Data Libraries. Examples of the Data Libraries on Galaxy-qld:
Human variation data
Human gene annotations
Human conservation data
Mouse gene annotations
Arabidopsis thaliana gene annotations

List of all Data Libraries

More information


Getting data into Galaxy-qld

This training material shows how to put user data into Galaxy-qld though different channels: though a link, from a password protected ftp server, using ftp and ftp client software, from aarnet CloudStor, using GenomeSpace Importer and Exporter tools. Examples of public data usage include built-in data such as aligner indices and SnpEff database, Galaxy Data Libraries, direct import from UCSC Table Browser and EMBL-EBI European Nucleotide Archive.

More information


RDS Beacon Tutorial server

This short presentation introduces RDS Beacon Tutorial server, a platform for sharing of human variation data without personal information. We provide detailed instructions for deployment of Beacon server on NeCTAR cloud.

More information