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Old 10-16-2012, 07:39 AM   #1
dan
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Default HTS Mappers!

Anyone vounteer to update the wiki ;-)

http://wwwdev.ebi.ac.uk/fg/hts_mappers/
http://dx.doi.org/10.1093/bioinformatics/bts605

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: nf@ebi.ac.uk
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Old 10-16-2012, 06:43 PM   #2
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A comparison of accuracy would have been nice...
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Old 10-17-2012, 01:17 AM   #3
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I was thinking to organize a 'mapathon' on the wiki.... how would you recommend benchmarking accuracy?
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Old 10-17-2012, 09:42 AM   #4
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Quote:
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...
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Old 10-18-2012, 12:57 AM   #5
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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...
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Old 10-18-2012, 10:48 AM   #6
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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.
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Old 10-19-2012, 08:41 AM   #7
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Should we generate data so we have a 'gold standard'? Or just work with metrics based on consistency, speed, and coverage?
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Old 10-19-2012, 08:58 AM   #8
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Are you talking about simulated or real?
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Old 10-20-2012, 12:54 PM   #9
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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?
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Old 10-20-2012, 01:01 PM   #10
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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.
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Old 10-20-2012, 01:16 PM   #11
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Fabulous! Please link to the datasets, and I'll try to put wheels in motion via the wiki :-)
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