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It's still a very important step for third generation sequencing machines. ...the HeliScope generates DNA sequence data as a massive collection of very short r

It's still a very important step for third generation sequencing machines. ...the HeliScope generates DNA sequence data as a massive collection of very short reads - but while the Illumina platform is now routinely generating reads over 100 bases long, the HeliScope generates reads on average just 32 bases long, with only a tiny fraction exceeding 50 bases in length. In fact, the reads are deliberately filtered to exclude any extending for over 70 bases, as these are highly enriched for technical artefacts. Stitching together a genome sequence with such short reads is a substantial challenge, especially in regions where the sequence is repetitive - and indeed the technology can only cover 90% of the reference genome compared to 99.9% for a genome recently sequenced to similar depth with Illumina. http://scienceblogs.com/geneticfuture/2009/08/first_human_genome_sequenced_u.php http://scienceblogs.com/geneticfuture/2009/08/first_human_ge... So they can still stitch together 90% of your genome within a month, and there's no reason to think this will not improve in the future.

dflock 17y ago
I would imagine that they could get the cost down and the speed up but I wouldn't imagine that the coverage would improve much if they continue to use short reads - i.e. small ~32 base bits of DNA. As I understand it, there's enough repetition and duplication in the genome that many of these little lengths are going to be identical: AAAA...AAAA or GGGAGGGA...GGGA etc. and that these little strips will match in many different places when placed alongside a fully assembled reference genome. They will also match and overlap a lot with each other. This means that you can't tell where they're supposed to go when you try to re-assemble your collection of little bits into a complete sequence. This means that you're always going to be left with a collection of bits left over that you have no way of placing into the sequence, hence less than 100% coverage. I guess you would need to be using reads long enough to ensure that each of your fragments was unique to get 100% coverage.
timr 17y ago
"It's still a very important step for third generation sequencing machines." It's a very important step for the PR department of Helicos. Unless they can dramatically increase the read length or reduce the error rate, this technology isn't going to be very useful. The genome is not randomly distributed, and there are lots of repeated elements that make assembly impossible with such short fragments of sequence. Even shotgun sequencing -- which has read lengths of hundreds of bases -- isn't good enough for the human genome. That said, the technology might be useful for something like large-scale SNP analysis, where (even though they've got error rates >1%), they could sequence the same genome dozens of times, and get an idea of the interesting variations. Maybe. But the current technology isn't very useful for genome sequencing and assembly.

dflock 17y ago

I would imagine that they could get the cost down and the speed up but I wouldn't imagine that the coverage would improve much if they continue to use short reads - i.e. small ~32 base bits of DNA. As I understand it, there's enough repetition and duplication in the genome that many of these little lengths are going to be identical: AAAA...AAAA or GGGAGGGA...GGGA etc. and that these little strips will match in many different places when placed alongside a fully assembled reference genome. They will also match and overlap a lot with each other. This means that you can't tell where they're supposed to go when you try to re-assemble your collection of little bits into a complete sequence. This means that you're always going to be left with a collection of bits left over that you have no way of placing into the sequence, hence less than 100% coverage. I guess you would need to be using reads long enough to ensure that each of your fragments was unique to get 100% coverage.

timr 17y ago

"It's still a very important step for third generation sequencing machines." It's a very important step for the PR department of Helicos. Unless they can dramatically increase the read length or reduce the error rate, this technology isn't going to be very useful. The genome is not randomly distributed, and there are lots of repeated elements that make assembly impossible with such short fragments of sequence. Even shotgun sequencing -- which has read lengths of hundreds of bases -- isn't good enough for the human genome. That said, the technology might be useful for something like large-scale SNP analysis, where (even though they've got error rates >1%), they could sequence the same genome dozens of times, and get an idea of the interesting variations. Maybe. But the current technology isn't very useful for genome sequencing and assembly.