Difference in pipeling designing for data analysis and output files generated by Sequencing by synthesis, Ion Torrent, and Pyrosequencing.

Question

[shuksi1984]

If I sequence a tissue/blood sample from the same subject (human), how will the outputs from Illumina's Genome analyzer, Roche 454's Genome Sequencer, and Applied Biosystem's SOLiD will differ in terms of accuracy, output file format, and output file size. I only want to know the difference between the output files generated by Sequencing by synthesis, Ion Torrent, and Pyrosequencing. Also, will there be any difference in pipeline designing for data analysis? According to my knowledge, Illumina provides cheapest sequencing service with an accuracy of 98% which is less than Roche 454 and Applied Biosystems.

[GenoMax]

No sequencing technology is perfect. Each has its own biases/errors. With Illumina the error rate is the lowest at this time (since the technology has been around for longer). Ion torrent is going to suffer from inability to distinguish between long homo-polymeric stretches. PacBio and Oxford Nanopore have high error rates (10-15%) but are able to use experimental (CCS sequencing) or informatics workarounds that can mitigate the error to some extent.

Most aligners will handle Illumina data just fine. I don't work much with Ion but there used to be an aligner(TMAP) that came with the machine that was likely tuned for Ion tech. minimap2 is probably the best aligner out there at this time for PacBio/Nanopore. It has data specific options that likely take error models for the two technologies in consideration when doing alignments. PacBio also makes blasr available for PacBio data.

[Devon Ryan]

You're unlikely to find either a Genome Analyzer, 454, or SOLiD machine still running these days and none of those are Ion Torrent...