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.