Seqanswers Leaderboard Ad



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

  • Software to process IonTorrent data

    Does anyone of you have experience with different softwares available for processing Ion Torrent data? Or could you recommend a certain software?

    I found these four also suggested on the Ion Torrent page:

    Important Features I'm looking for:

    - handling of RNA "AND" DNA data
    - consensus calling, if possible quality-aware
    - SNP and Indel (marker) detection
    - comparisons of sequences to detect things like inversions etc.
    - if possible: is there a software where one can upload or directly align reads to an existing reference (genome or scaffolds?)!!? -> that would be great
    - possible statistical analyses
    - graphical (output) applications

    I cannot tell from the descriptions of the different software, which one is the "best".
    What also influences my choice positively is a user-friendly interface and a software.

    What do you recommend?

  • #2
    Why not request evaluation copies of all of them? And get some prices? Better to try them out and make sure that not only they do what you want, but in the time you want and with the ease you desire. There's no 'best fit' solution for everyone.


    • #3
      Unless you are willing to purchase commercial software (which is what the four examples on that page are) why not use galaxy (


      • #4
        I've used Real Time Genomics with ion torrent data, it is commercial but there is a free verion for individual use. It's very fast, and easy to use, works on ion torrent + 454 and Illumina data. With the ion torrent data I've got it takes a few minutes to map it to the reference genome.

        Real Time Genomics provides bioinformatic services and analytical solutions that reduce the cost and complexity of extracting knowledge from raw genomic data.


        • #5
          LifeTech just released their assembler as open source on GitHub. Here's their announcement, copied from http://lifetech-it.hosted.jivesoftwa.../docs/DOC-2431 (free registration required to see the announcement, not to get the software):
          Torrent Suite 2.0 Source Code
          VERSION 1
          Created on: Jan 23, 2012 1:37 PM by Matt Dyer - Last Modified: Jan 23, 2012 1:40 PM by Matt Dyer

          I am happy to annouce that the source code for Torrent Suite 2.0, TMAP, Torrent Scout, and the new Ion Variant Caller plugin are now available publically at GitHub. Anyone interested in the source code should get it from GitHub, we will not longer post the source on the community.

          Torrent Suite 2.0:


          Torrent Scout:

          Torrent Variant Caller Plugin:

          If you are interested in sharing your changes to our source with the community please see Sharing your Torrent Suite modifications with the Community ( )
          Last edited by PenelopeFudd; 02-14-2012, 10:50 AM. Reason: clarify that the software doesn't need registration


          Latest Articles


          • seqadmin
            Best Practices for Single-Cell Sequencing Analysis
            by seqadmin

            While isolating and preparing single cells for sequencing was historically the bottleneck, recent technological advancements have shifted the challenge to data analysis. This highlights the rapidly evolving nature of single-cell sequencing. The inherent complexity of single-cell analysis has intensified with the surge in data volume and the incorporation of diverse and more complex datasets. This article explores the challenges in analysis, examines common pitfalls, offers...
            06-06-2024, 07:15 AM
          • seqadmin
            Latest Developments in Precision Medicine
            by seqadmin

            Technological advances have led to drastic improvements in the field of precision medicine, enabling more personalized approaches to treatment. This article explores four leading groups that are overcoming many of the challenges of genomic profiling and precision medicine through their innovative platforms and technologies.

            Somatic Genomics
            “We have such a tremendous amount of genetic diversity that exists within each of us, and not just between us as individuals,”...
            05-24-2024, 01:16 PM





          Topics Statistics Last Post
          Started by seqadmin, 06-07-2024, 06:58 AM
          0 responses
          Last Post seqadmin  
          Started by seqadmin, 06-06-2024, 08:18 AM
          0 responses
          Last Post seqadmin  
          Started by seqadmin, 06-06-2024, 08:04 AM
          0 responses
          Last Post seqadmin  
          Started by seqadmin, 06-03-2024, 06:55 AM
          0 responses
          Last Post seqadmin