Wednesday 14 July 2010

the nuts and bolts behind ABI's SAET

I really do not like to use tools that I have no idea what they are trying to do. 
ABI's SAET SOLiD™ Accuracy Enhancer Tool (SAET) is a one example that had extremely brief documentation except what it promised to do 

  • The SOLiD™ Accuracy Enhancer Tool (SAET) uses raw data generated by SOLiD™ Analyzer to correct miscalls within reads prior to mapping or contig assembly.  
  • Use of SAET, on various datasets of whole or sub-genomes of < 200 Mbp in size and of varying complexities, readlengths, and sequence coverages, has demonstrated improvements in mapping, SNP calling, and de novo assembly results.
  • For denovo applications, the tool reduces miscall rate substantially

    Recently attended an ABI's talk and finally someone explained it in a nice diagram. It is akin to Softgenetic's condensation tool.( I made the link ). Basically, it groups reads by similarity and where they find a mismatch that is not supported by high quality reads they correct the low quality read to reach a 'consensus'. I see it as a batch correction of sequencing errors which one can typically do by eye (for small regions). This correction isn't without its flaws. I now understand why such an error correction isn't implemented on the instrument. And is presented as a user choice. My rough experience with this tool is that it increases mapping by ~ 10% how this 10% would affect your results is debatable.

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