Comments for Pathogens: Genes and Genomes http://pathogenomics.bham.ac.uk/blog A heady mix of bacterial pathogenomics, next-generation sequencing, type-III secretion, bioinformatics and evolution! Fri, 19 Mar 2010 07:48:24 +0000 http://wordpress.org/?v=2.8.5 hourly 1 Comment on Amerithrax case closed thanks to forensic genomics (and lots of other leg work) by Mark Pallen http://pathogenomics.bham.ac.uk/blog/2010/03/amerithrax-case-closed-thanks-to-forensic-genomics-and-lots-of-other-leg-work/comment-page-1/#comment-59298 Mark Pallen Fri, 19 Mar 2010 07:48:24 +0000 http://pathogenomics.bham.ac.uk/blog/?p=283#comment-59298 See also, from this week's Science Magazine: <a href="http://www.sciencemag.org/cgi/content/full/327/5972/1435" rel="nofollow">Silicon Mystery Endures in Solved Anthrax Case</a> See also, from this week’s Science Magazine:
Silicon Mystery Endures in Solved Anthrax Case

]]> Comment on ABI challenge Sanger Centre’s decision to return their instruments by Pathogens: Genes and Genomes » Illumina still dominate sequencing market: ABI and 454 Jockey for 2nd Place http://pathogenomics.bham.ac.uk/blog/2009/08/abi-challenge-sanger-centre/comment-page-1/#comment-59295 Pathogens: Genes and Genomes » Illumina still dominate sequencing market: ABI and 454 Jockey for 2nd Place Thu, 18 Mar 2010 14:49:18 +0000 http://pathogenomics.bham.ac.uk/blog/?p=73#comment-59295 [...] huge amount of ground in the past year or two. Pretty good for a machine we wrote off as being the “worst of both worlds” last August. It is not clear to me how they have managed this impressive feat (although I have [...] [...] huge amount of ground in the past year or two. Pretty good for a machine we wrote off as being the “worst of both worlds” last August. It is not clear to me how they have managed this impressive feat (although I have [...]

]]> Comment on Experiencing suboptimal 454 runs and slow Roche deliveries? You are not alone! by Mark Pallen http://pathogenomics.bham.ac.uk/blog/2010/03/experiencing-suboptimal-454-runs-and-roche-deliveries-you-are-not-alone/comment-page-1/#comment-59293 Mark Pallen Sat, 13 Mar 2010 09:14:24 +0000 http://pathogenomics.bham.ac.uk/blog/?p=260#comment-59293 Just for the record our most recent delivery and run went OK, which is reassuring. But the lingering anxiety that the problems might recur remains. If any other readers continue to experience similar problems, please let us know. Just for the record our most recent delivery and run went OK, which is reassuring. But the lingering anxiety that the problems might recur remains. If any other readers continue to experience similar problems, please let us know.

]]> Comment on Experiencing suboptimal 454 runs and slow Roche deliveries? You are not alone! by Aziz Aboobaker http://pathogenomics.bham.ac.uk/blog/2010/03/experiencing-suboptimal-454-runs-and-roche-deliveries-you-are-not-alone/comment-page-1/#comment-59292 Aziz Aboobaker Fri, 12 Mar 2010 19:12:45 +0000 http://pathogenomics.bham.ac.uk/blog/?p=260#comment-59292 yes... well we have been told its fluidics... But we think its chemistry... or at least chemistry as well. thanks for sharing By the way please all come to the UK NExt Gen meeting in Nottingham on August 12th/13th in Nottingham. I'll send out information about it at the beginning of April yes… well we have been told its fluidics… But we think its chemistry… or at least chemistry as well.

thanks for sharing

By the way please all come to the UK NExt Gen meeting in Nottingham on August 12th/13th in Nottingham. I’ll send out information about it at the beginning of April

]]> Comment on Landed: First Illumina HiSeq Machines Advertised by Pathogens: Genes and Genomes » A triumph for Old World genomics http://pathogenomics.bham.ac.uk/blog/2010/02/landed-first-illumina-hiseq-machines-advertised/comment-page-1/#comment-59290 Pathogens: Genes and Genomes » A triumph for Old World genomics Mon, 08 Mar 2010 17:27:13 +0000 http://pathogenomics.bham.ac.uk/blog/2010/02/landed-first-illumina-hiseq-machines-advertised/#comment-59290 [...] 600 gigabase pairs sounds like a lot, but this could be completed in just three runs of the new Illumina Hi-Seq instrument! It makes you wonder whether future studies will need quite so many [...] [...] 600 gigabase pairs sounds like a lot, but this could be completed in just three runs of the new Illumina Hi-Seq instrument! It makes you wonder whether future studies will need quite so many [...]

]]> Comment on Tips for de novo bacterial genome assembly by nat http://pathogenomics.bham.ac.uk/blog/2009/09/tips-for-de-novo-bacterial-genome-assembly/comment-page-1/#comment-59289 nat Wed, 17 Feb 2010 09:08:05 +0000 http://pathogenomics.bham.ac.uk/blog/?p=158#comment-59289 Hi Nick, Very useful tips, thanks! About velvet's behavior of not recalling the consensus, which Daniel confirmed to me as still being the case in latest velvets, I was wondering: Does this mean that for a given genomic paired-end assembly , the whole contigs.fa file needs to be updated using the RecalConsensus tip you described (as the file is somewhat 'wrong')? This also implies converting each contig into a bank, recalling the consensus and getting back to a new fasta? I am saying this because I have fungal genomes to handle, their assemblies are not loadable to amos (for bank conversion) as a whole, only splitting to separate contigs the afg file works.. Maybe this was not the case for your bacterial genomes? Or is there any other tip I am missing? This issue, if I get it right, seems quite important, however I ve only found it mentionned in this blog... I am wondering whether the published velvet genomes are recalled Consensus ones or not... Kind regards, Natassa Hi Nick,
Very useful tips, thanks! About velvet’s behavior of not recalling the consensus, which Daniel confirmed to me as still being the case in latest velvets, I was wondering: Does this mean that for a given genomic paired-end assembly , the whole contigs.fa file needs to be updated using the RecalConsensus tip you described (as the file is somewhat ‘wrong’)?
This also implies converting each contig into a bank, recalling the consensus and getting back to a new fasta? I am saying this because I have fungal genomes to handle, their assemblies are not loadable to amos (for bank conversion) as a whole, only splitting to separate contigs the afg file works.. Maybe this was not the case for your bacterial genomes? Or is there any other tip I am missing?
This issue, if I get it right, seems quite important, however I ve only found it mentionned in this blog… I am wondering whether the published velvet genomes are recalled Consensus ones or not…
Kind regards,
Natassa

]]> Comment on New Illumina Announced – BGI to become world’s largest genome centre by Science Report » Blog Archive » Genome Sequencing Under $10,000 http://pathogenomics.bham.ac.uk/blog/2010/01/new-illumina-announced-bgi-to-become-worlds-largest-genome-centre/comment-page-1/#comment-59280 Science Report » Blog Archive » Genome Sequencing Under $10,000 Mon, 18 Jan 2010 09:30:43 +0000 http://pathogenomics.bham.ac.uk/blog/?p=234#comment-59280 [...] Pathogens [...] [...] Pathogens [...]

]]> Comment on New Illumina Announced – BGI to become world’s largest genome centre by Genome Sequencing Under $10,000 « ScienceRoll http://pathogenomics.bham.ac.uk/blog/2010/01/new-illumina-announced-bgi-to-become-worlds-largest-genome-centre/comment-page-1/#comment-59279 Genome Sequencing Under $10,000 « ScienceRoll Sun, 17 Jan 2010 12:14:24 +0000 http://pathogenomics.bham.ac.uk/blog/?p=234#comment-59279 [...] Pathogens [...] [...] Pathogens [...]

]]> Comment on Announcement: xBASE Annotation Service by herm http://pathogenomics.bham.ac.uk/blog/2009/12/announcement-xbase-annotation-service/comment-page-1/#comment-59278 herm Fri, 15 Jan 2010 05:08:00 +0000 http://pathogenomics.bham.ac.uk/blog/?p=195#comment-59278 Hi Nick, I suggest you could consider using Aragorn for annotation of ncRNA. It's faster than tRNAScan-SE and identifies tmRNA too. Hi Nick, I suggest you could consider using Aragorn for annotation of ncRNA. It’s faster than tRNAScan-SE and identifies tmRNA too.

]]> Comment on New Illumina Announced – BGI to become world’s largest genome centre by The Future of Second Generation Sequencing « Genetic Inference http://pathogenomics.bham.ac.uk/blog/2010/01/new-illumina-announced-bgi-to-become-worlds-largest-genome-centre/comment-page-1/#comment-59277 The Future of Second Generation Sequencing « Genetic Inference Wed, 13 Jan 2010 12:51:29 +0000 http://pathogenomics.bham.ac.uk/blog/?p=234#comment-59277 [...] detail about the machine: for that, see posts at Genomics Law Report, Genome Web, Genetic Future, Pathogenomics and PolITiGenomics. What I really care about is what this machine implies for the future of [...] [...] detail about the machine: for that, see posts at Genomics Law Report, Genome Web, Genetic Future, Pathogenomics and PolITiGenomics. What I really care about is what this machine implies for the future of [...]

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