Meg - if you are having problems with assembling your phages, please contact me off this list, and I will point you to a colleague who assembles phage genomes on a daily basis. He's a friendly and helpful guy.
Thank you for answering Meg's questions. Almost all the data I work with is produced internally so I always have the raw formats available. I'm not used to dealing with people who don't work this way.
Our public health lab decided that it was cheaper to outsource our sequencing rather than buy and run a sequencer so I have had to deal with six or seven sequencing centres from Montreal to Rotterdam this year. Without fail, the 454 centres just supply the contigs from Newbler as a single fasta file.
It drives me crazy because the bench scientists treat them as gospel and use them without any further checking. It's not their fault as they do not know better. The sequencing centres should realise this and be a bit more professional at telling their clients exactly what it is that they are getting.
And some bench scientists should not be so arrogant and realise that they do need proper bioinformatic straining.
bioinformatic straining - "bioinformatics training". Freudian slip?
I agree that you have to be wary of contigs results without data to back them up. None of the assemblers are perfect and I know from personal experience that even good looking results can have serious flaws.
At least here at work we have all the data, the samples themselves and experienced people who can double check the results.
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