Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • Ion Torrent and Whole Exome Sequence

    Hi all,

    I am a new user of an Ion Torrent and we are working on Whole Exome Sequencing (WES). From what I've read so far, GATK is the golden standard for such analysis when it comes to Illumina data BUT that does not apply so much to Ion Torrent data.
    Does anyone have experience on WES with Ion Torrent and can help me by proposing software to use for my pipeline, or alterations on the GATK best practice?

    Thank you in advance for your time

  • #2
    Far from being a master in the field...Have you had a look at Ion Reporter?

    Comment


    • #3
      Well actually I have, but I am trying to find something open-source and not specifically from the producer (LifeTech).

      Comment


      • #4
        You can generate FastQ files on the Ion Torrent. I would just use GATK.

        The Broad has published ChIP-Seq on the PGM and they must have used GATK.

        Comment


        • #5
          GATK does not align reads so what do you use for this?

          Torrent Suite. Contribute to iontorrent/TS development by creating an account on GitHub.


          Is open source TorrentSuite, contains a aligner and variant caller.

          Comment


          • #6
            The Torrent Suite has specific settings for exome analysis already. I'm not sure why you would want to use other tools.

            Comment


            • #7
              Thank you for the suggestion. I will definitely try TorrentSuite!

              Do you know if it the same software as the one running on Ion Proton?

              Comment


              • #8
                AFAIK: Torrent suite download available on github does not include Ion reporter (which is not free software). If you have access to an ion machine then there is likely to be a copy there that you can use for the variant calling/coverage analysis.

                Comment


                • #9
                  Thank you, I'll look into it.

                  Comment


                  • #10
                    Originally posted by alexdem View Post
                    Thank you for the suggestion. I will definitely try TorrentSuite!

                    Do you know if it the same software as the one running on Ion Proton?
                    Yes, TS is the same as what is running your Ion Proton.
                    Brian

                    Comment


                    • #11
                      Ion reporter uses gatk doesn't it? Very little of the Ion torrent software is made by lifetech, most of it is just the freely available software with the default settings tweaked for torrent data.

                      Comment


                      • #12
                        I'm not sure what Ion Reporter uses, but the torrent server uses TMAP to align reads.

                        Comment


                        • #13
                          Originally posted by BrianJames View Post
                          I'm not sure what Ion Reporter uses, but the torrent server uses TMAP to align reads.
                          Yeah, but TMAP is basically just a wrapper for BWA with the defualt being BWA fastmap.

                          Comment


                          • #14
                            TMAP is mostly BWA but it runs it in an iterative process. It also takes their flow bam files. I almost always see more data aligning with TMAP.

                            Ion Reporter and the server uses the same alignment and variant calling tools. The reporter software adds database annotation to the variants called with FreeBayes.

                            Comment


                            • #15
                              We have had success using GSNAP to map Ion Torrent reads -especially for RNAseq with splicing. Tophat2/Bowtie2 do not deal well with Ion Torrent data.

                              Comment

                              Latest Articles

                              Collapse

                              • seqadmin
                                Strategies for Sequencing Challenging Samples
                                by seqadmin


                                Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
                                03-22-2024, 06:39 AM
                              • seqadmin
                                Techniques and Challenges in Conservation Genomics
                                by seqadmin



                                The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

                                Avian Conservation
                                Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
                                03-08-2024, 10:41 AM

                              ad_right_rmr

                              Collapse

                              News

                              Collapse

                              Topics Statistics Last Post
                              Started by seqadmin, 03-27-2024, 06:37 PM
                              0 responses
                              16 views
                              0 likes
                              Last Post seqadmin  
                              Started by seqadmin, 03-27-2024, 06:07 PM
                              0 responses
                              13 views
                              0 likes
                              Last Post seqadmin  
                              Started by seqadmin, 03-22-2024, 10:03 AM
                              0 responses
                              57 views
                              0 likes
                              Last Post seqadmin  
                              Started by seqadmin, 03-21-2024, 07:32 AM
                              0 responses
                              70 views
                              0 likes
                              Last Post seqadmin  
                              Working...
                              X