Hi, Do you know of any recent reviews of NGS aligners? I can only find the classic review http://bib.oxfordjournals.org/content/11/5/473.abstract, which is rather old.
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Have a look at http://bioinformatics.oxfordjournals...ent/28/24/3169 -
The Assemblathon 2 paper at arXiv.org (here) does a good job of evaluating performance of various assemblers.Comment
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Thanks all, I'm more interested in finding a review of short read aligner methods rather than performance. I'm a bit surprised such a review is not readily available in recent times. http://arxiv.org/abs/1304.5952 is a link for RNA-seq survey for anyone interested.Comment
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Aligners, not assemblers? Sorry, I responded before the second cup of coffee kicked in. Usually, the most current alignment publications include a comparison to earlier software. Some of the most recent are LAST (available here), Subread (here), and BWA-MEM (here). All contain comparative metrics. You can also run your own comparisons of some programs at this website.Comment
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While the performance of NGS mappers keeps improving, the methodologies have not been changed much in the past few years. The biggest shift is that we more often adopt/adapt old-school algorithms developed for Sanger reads. With a few exceptions (e.g. GEM), most recent mappers use the Blast-like algorithm. We still see improvements, IMHO, partly because we are better at implementation, and partly because we are comparing new 100bp algorithms to old 36bp algorithms applied on 100bp+ reads.Comment
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