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NGS Analyses in Galaxy

Galaxy team is announcing the launch of the first free public resource for NGS analysis. This service is the beginning of our campaign to provide free web-based utilities for NGS analysis and later in the year will take advantage of the Cloud resources. At present, there are three main groups of tools including:

  1. NGS QC and manipulation - contains a variety if tools for dealing with all flavors of fastq datasets as well as outputs of SOLiD and 454 instruments.

  2. NGS Mapping - currently includes bowtie (Illumina & SOLiD), BWA (Illumina), and lastz (454) mappers. PerM (SOLiD) is on the way and more will be added in the coming months. Transcriptome tools are also in the final stages of development.

  3. NGS SAMTools - includes a variety of utilities for SAM/BAM manipulation. Some are based on SAMtools library, some are written by Galaxy team.

Galaxy team does not like to read documentation and expects that others don't either. This is why we make short movies called quickies. To see what Galaxy can do, see these:

  • Example 1 - mapping mate-paired SOLiD data
  • Example 2 - mapping SOLiD (or Illumina) data against a custom genome
  • Example 3 - mapping paired-end Illumina run and visualizing results at UCSC Browser.

Enjoy and send us feedback! Those who want to contribute tools, brains, or coding skills, consider attending Galaxy Developer Conference. We might sponsor your participation!

This free service is brought you by NIH (NHGRI), NSF, the Huck Institutes for the Life Sciences and the Institute for CyberScience at Penn State University, Emory University and the Pennsylvania Department of Public Health.