Announcement

Collapse
No announcement yet.

Assembly of viral quasispecies

Collapse
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • Assembly of viral quasispecies

    Hi all,

    Has anyone found software or software settings that work well for assembly of viral quasispecies from 454 reads? Newbler on default settings doesn't work at all well, breaking up into large numbers of very short contigs.

    There is an interesting package called "Q Assembler" but this doesn't seem to have been released (http://www.bioinformatics.org/qassembler/wiki/).

    Any help appreciated

    Nick

  • #2
    Hello Nick

    I am looking for a similar solution. Did you happen to come across anything helpful ?

    Sowmya

    Comment


    • #3
      Hiya,
      I use CLCbio's denovo assembler with the following settings for plant viruses: MM=2,I=3,D-3, Length fraction =0.5, Similariity 0.9. Seems to work pretty well (so far!) especially as we're sequencing direct from the host to get the viral genomes.
      Hope that helps,
      Rach
      Last edited by rglover; 05-04-2010, 12:13 AM.

      Comment


      • #4
        That's good to know. I didn't find anything that particularly helped, although I did briefly consider using PyroNoise on some PCR amplicons from a viral source.

        Comment


        • #5
          have you looked at this?
          Characterization of Quasispecies of Pandemic 2009 Influenza A Virus (A/H1N1/2009) by De Novo Sequencing Using a Next-Generation DNA Sequencer
          http://www.plosone.org/article/info:...l.pone.0010256

          and
          velvet
          http://www.ebi.ac.uk/~zerbino/velvet/
          http://kevin-gattaca.blogspot.com/

          Comment


          • #6
            most folk don't rather like the poetry that tons of and plenty of people ignore it to not tell everyone tho' so I helped the oldsters to understand it higher during a} very fully completely different technique as different websites do resembling login here where you'll be able to win 100 gift card at a survey that helps to form your life easier.

            Comment

            Working...
            X