Exome Sequence Work Flow

Question

[Raju]

Is there any GUI linked work flow for Exome seq analysis. I have aligned Fastq files with BWA and would like to compare normal with tumor to find out mutations.

Thanks

Answer 1

[DG]

Galaxy is an excellent option as already suggested. If you want to do it in the cloud Seven Bridges Genomics has an interesting platform and includes some common Exome-Seq pipelines prebuilt. They give you $250 in "startup funds" for running analyses which is enough for several exomes. I've tested three samples and I don't think it even used half of my funds in compute time.

[zx8754]

There are many other providers, see List of Cloud Genomics companies

[DG]

Yes of course there are many other providers. I wasn't trying to be exhaustive and chose to mention one in particular that I have actually used. And not all of the cloud genomics companies have curated lists of workflows.

Answer 2

[Björn]

You can use Galaxy with variouse tools if you like. You can install Galaxy locally or use any of the public available ones. GATK2, samtools, snpeff are all available through the Tool Shed.