Entering edit mode
5.9 years ago
adam.nunn
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0
Does anybody have recommendations for current tools similar to RazerS3 in this regard, particularly that handle PE reads and output to SAM format but this is not strictly necessary.
If by "full sensitivity" you are looking for an "all-mapper" as defined on RazerS3 paper, there is BitMapper, FEM, Hobbes, mrFAST, SHRiMP2 and Yara. I never used any of them, tough.
edit: added FEM.
I used Shrimp2 for SOLiD back in the day I believe (2011). Pretty poor. mrFAST was far, far worse. We should be very glad to have tools like bwa, STAR, and bowtie2. Just my two cents. Novoalign allows a lot of parameter tuning, but is commercial. Segemehl http://hoffmann.bioinf.uni-leipzig.de/LIFE/segemehl.html might also fit your bill.
But are the aligners at fault, or is it the data? Though I haven't dealt a lot with SOLiD, all data sets I've seen were bad.
Anyway, you are right in the "best-mappers" won against the "all-mappers", they generally give better (or good enough) results a lot faster.
@adam.nunn, beware of the requirements from the mapper you choose. For example, mrFAST (and maybe BitMapper) requires allreads to be same length, that is, no adapter trimming can be performed - you either don't trim adapters, or discard reads with adapters.
Thanks for the suggestions! Specifically I'm looking for all-mappers that are capable of finding every single occurrence of a read within a tolerated edit or Hamming distance, ie no trade-offs for performance reasons. For working with illumina reads of 100-150 bp approximately.
bbmap.shfrom BBMap suite can probably do that well. There are a ton of options and you will need to experiment.Please do not post the same comment twice. If people keep asking for details means that your comment was not clear.
It is unclear what you mean with 'full sensitivity', and what your application is. The recommendations for aligners would be quite different if you have short read Illumina WGS, RNA-seq or long read nanopore/PacBio data.
Please elaborate. As far as I know all modern aligners can handle PE reads and support SAM format.
Ah yes, sorry. I'm looking for all-mappers that are capable of finding every single occurrence of a read within a tolerated edit or Hamming distance, ie no trade-offs for performance reasons. For working with illumina reads of 100-150 bp approximately.