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  • 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

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    • #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.

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      • #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.

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        • #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
          Pandemic 2009 influenza A virus (A/H1N1/2009) has emerged globally. In this study, we performed a comprehensive detection of potential pathogens by de novo sequencing using a next-generation DNA sequencer on total RNAs extracted from an autopsy lung of a patient who died of viral pneumonia with A/H1N1/2009. Among a total of 9.4×106 40-mer short reads, more than 98% appeared to be human, while 0.85% were identified as A/H1N1/2009 (A/Nagano/RC1-L/2009(H1N1)). Suspected bacterial reads such as Streptococcus pneumoniae and other oral bacteria flora were very low at 0.005%, and a significant bacterial infection was not histologically observed. De novo assembly and read mapping analysis of A/Nagano/RC1-L/2009(H1N1) showed more than ×200 coverage on average, and revealed nucleotide heterogeneity on hemagglutinin as quasispecies, specifically at two amino acids (Gly172Glu and Gly239Asn of HA) located on the Sa and Ca2 antigenic sites, respectively. Gly239 and Asn239 on antigenic site Ca2 appeared to be minor amino acids compared with the highly distributed Asp239 in H1N1 HAs. This study demonstrated that de novo sequencing can comprehensively detect pathogens, and such in-depth investigation facilitates the identification of influenza A viral heterogeneity. To better characterize the A/H1N1/2009 virus, unbiased comprehensive techniques will be indispensable for the primary investigations of emerging infectious diseases.


          and
          velvet
          http://kevin-gattaca.blogspot.com/

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