AGRF LAB

Welcome to the Galaxy Australia AGRF Lab!

Bootstrap Grid

Import data

  • Find your data at the AGRF Hub.
  • Download this data to your computer.
  • Upload data from your computer to Galaxy.

Note: Galaxy and the AGRF Hub are not configured for long-term data storage. Ensure you save raw and processed data to a secure archive.

  • After uploading data, we recommend compressing fastq and fasta files.
  • This will save you time and storage space.

  • Galaxy Australia is free to use.
  • Get started with these user-friendly tutorials.

Request support, new tools, or additional storage.

Contact AGRF for more help with your data.

Quality control

Assess the quality and characteristics of your raw sequencing data, and perform data cleaning prior to analysis.

  • Galaxy has a range of tools available to perform quality control.

  • Select your datatype in the tabs above to see relevant tools and workflows.

Some tools require data in different formats. Learn about converting between bam, fastq and fastqsanger formats, and compressing/uncompressing files.

Generate a range of reports about raw data quality and characteristics.

Input data:

fastq
fastq.gz

This tool is faster than FastQC, and can also trim reads and filter by quality.

Input data:

fastqsanger
fastqsanger.gz

QC of paired-end Illumina data.

Tools: FastQC MultiQC

Run this workflow first if your raw data is in css.bam format.

Tools: SamToFastq Samtools flagstat

Filter for adapter contamination.

Tools: HiFiAdapterFilt

A plotting suite for long read sequencing data and alignments.

Input data:

fastq
fastq.gz

Filter reads based on quality, length, or GC content.

Input data:

fastqsanger

Data analysis

  • Analysis options depend on your research aims and the type of sequencing data (e.g. DNA or RNA, short-read or long-read).
  • Galaxy has a range of tools installed for different types of analyses.
  • Select your research area in the tabs above to see relevant tools and workflows.

Contact us to request installation of new tools or reference datasets.

Tutorial

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This wf does xyz

Tutorial

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Tutorial

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Thanks for checking out the Galaxy Australia AGRF Lab!

AGRF is the Australian Genome Research Facility.
Order more sequencing from AGRF

Contact Galaxy Australia.

Connect with the Australian genomics community.

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Contributors