Assembling Illumina and 454 data
This is a question that keeps cropping up on Seqanswers and Biostar. Amazingly there is still no 100% satisfactory pipeline for assembling combined Illumina and 454 data de novo. Here are the ways I know about: 1) Assemble 454 data on its own and correct with Illumina data For example, Newbler for the 454 data. [...]
Why filter SNPs which align on both strands?
A quick learning point for those grappling out with genome alignments, BAM/SAM files and SNP detection. When aligning short-read paired-end data against a reference, you can often end up with spurious SNP calls as a result of insertions or deletions when comparing your sequence to a reference. This is what it looks like (visualised via [...]
A few more MiSeq nuggets
Following on from Wednesday’s post on the HiSeq, I had the opportunity to quiz Neil Ward from Illumina further about the MiSeq. A few notes from our conversation. One thing people on Seqanswers.com were curious about is how the machine has become so much quicker than the HiSeq. This is mainly down to the reduced [...]
Genome sequencing platforms compared for bacterial de novo assemblies
Wow, I haven’t blogged for ages. Partly this is the usual excuse of not having time, and partly a lack of inspiration. Sorry. Perhaps just before Xmas is the wrong time to get my mojo back, but I guess that’s the way life is. So what’s been happening? Well, on the sequencing front we’ve recently [...]
Gazelles, elephants, blue whales and dodos: next-generation sequencing at the zoo
The big news today is that Life Tech, of SOLiD fame intend to acquire Ion Torrent, subject to certain technical milestones being reached. The best blog coverage is at Omics Omics and Genetic Future. This means Illumina, Life Tech and Roche, our sequencing Big Three have all now got into bed with “next-next-generation” technology platforms. [...]
Illumina still dominate sequencing market: ABI and 454 Jockey for 2nd Place
Yesterday, we launched a new version of the high-throughput sequencing map. I promised when it launched that when sufficient updates were received we would release instrument statistics. We have now received 214 updates from the community – thank you so much! So, without further ado, check out the statistics tables! Some bottom-line numbers: there are [...]
Landed: First Illumina HiSeq Machines Advertised
In case you didn’t see the announcement already, the Illumina HiSeq can produce 200 gigabases of sequence data and 2 billion reads per run. When it was launched we knew that BGI in China had signed an agreement to buy 128 of these machines but no-one has fessed up to owning one just yet. Things [...]
New Illumina Announced – BGI to become world’s largest genome centre
The ritual of checking Twitter with my coffee this morning brought much excited chattering about the new Illumina sequencer, the HiSeq 2000 which was announced yesterday. I won’t cover this in detail as there are already great blog posts up from Daniel McArthur, David Dooling and Genomics Lawyer. Bottom-line: $650,000 for the machine, $10,000 for [...]
Sequencing in the U.K.
James Hadfield has created a very nice community curated map of all known next-generation sequencing facilities. Although perhaps not 100% accurate it gives a good feel for the relative adoption of 454, Solexa and ABI in the UK. I’ve summarised the table as of today (plus adding in Birmingham’s new 454 machine). Excluding the Sanger [...]