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
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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
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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.
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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.
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