Keith blogs about the publicly avail 314 chip data with tantalizing 250+ bp read lengths
Ion Throws A Long Punch At MiSeq
The benchtop sequencer wars are heating up! Illumina and Life are engaged in a fierce war of pamphlets and datasets to convince the world that they have the edge. I won't attempt to give a complete play-by-play, but hit on the latest developments, which includes Ion releasing a dataset of 250+ bp reads.
Ion is coming out slugging with a new 314 dataset and application note, showing read lengths of over 250 bases (they assure me that it will work also on the 316, but nothing would beat a dataset!). This is long awaited; as I've noted before for applications such as amplicon sequencing the current fragment sizes of <150 bases and read lengths mostly in the 70s are challenging to work with. For my own applications, 250 is actually a very good number. When working with formalin-fixed, paraffin-embedded cancer samples, the recovered DNA is generally already sheared to about 450 bases, so you need to design smaller amplicons for good luck. A bit of 200 will cover many exons quite well (some common longer ones will require two amplicons; there are of course monsters out there that are special cases requiring many) and still leave room for a barcode. In my analysis of this dataset, Ion has an aligned read depth of over 200K at position 240 (below).
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Ion is coming out slugging with a new 314 dataset and application note, showing read lengths of over 250 bases (they assure me that it will work also on the 316, but nothing would beat a dataset!). This is long awaited; as I've noted before for applications such as amplicon sequencing the current fragment sizes of <150 bases and read lengths mostly in the 70s are challenging to work with. For my own applications, 250 is actually a very good number. When working with formalin-fixed, paraffin-embedded cancer samples, the recovered DNA is generally already sheared to about 450 bases, so you need to design smaller amplicons for good luck. A bit of 200 will cover many exons quite well (some common longer ones will require two amplicons; there are of course monsters out there that are special cases requiring many) and still leave room for a barcode. In my analysis of this dataset, Ion has an aligned read depth of over 200K at position 240 (below).
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