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  • HTS Mappers!

    Anyone vounteer to update the wiki ;-)




    Motivation: A ubiquitous and fundamental step in high-throughput sequencing analysis is the alignment (mapping) of the generated reads to a reference sequence. To accomplish this task numerous software tools have been proposed. Determining the mappers that are most suitable for a specific application is not trivial.

    Results: This survey focuses on classifying mappers through a wide number of characteristics. The goal is to allow practitioners to compare the mappers more easily and find those that are most suitable for their specific problem.

    Availability: A regularly updated compendium of mappers can be found at http://wwwdev.ebi.ac.uk/fg/hts_mappe...g/hts_mappers/.

    Contact: [email protected]
    Homepage: Dan Bolser
    MetaBase the database of biological databases.

  • #2
    A comparison of accuracy would have been nice...

    Comment


    • #3
      I was thinking to organize a 'mapathon' on the wiki.... how would you recommend benchmarking accuracy?
      Homepage: Dan Bolser
      MetaBase the database of biological databases.

      Comment


      • #4
        Originally posted by dan View Post
        I was thinking to organize a 'mapathon' on the wiki.... how would you recommend benchmarking accuracy?
        That would be AWESOME! I think we should query SEQanswers folks and vote on a number of metrics... this would be fun group project...

        Comment


        • #5
          Cool! It shouldn't be too hard either, but we need to have clear guidelines about what to measure and how, so that results are comparable across mappers. The only other thing we need is a dataset and a place to host it...
          Homepage: Dan Bolser
          MetaBase the database of biological databases.

          Comment


          • #6
            I'd recommend using % reads mapped and the # of reads mapped uniquely as part of the evaluation, and keep in mind that the # of known heterozygotes is a measure of sensitivity, NOT accuracy. My two cents.

            Comment


            • #7
              Should we generate data so we have a 'gold standard'? Or just work with metrics based on consistency, speed, and coverage?
              Homepage: Dan Bolser
              MetaBase the database of biological databases.

              Comment


              • #8
                Are you talking about simulated or real?

                Comment


                • #9
                  Simulated reads from real genomes.

                  We could simulate a range of 'noise' across a series of error models and produce reads characteristic of a variety of technologies... there must be software to do this already right?
                  Homepage: Dan Bolser
                  MetaBase the database of biological databases.

                  Comment


                  • #10
                    There is and we have these datasets already. I would be happy to share. We did a number of tests with this dataset for a manuscript we are sending out.

                    Comment


                    • #11
                      Fabulous! Please link to the datasets, and I'll try to put wheels in motion via the wiki :-)
                      Homepage: Dan Bolser
                      MetaBase the database of biological databases.

                      Comment

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