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Aligning contigs w.rt reference sequence

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  • Aligning contigs w.rt reference sequence

    Hello everyone,

    I am posting a very basic question. I am sorry if this is a repetition..but please give me an answer. We have sequenced some BAC clones and are now in the process of aligning them. I have tried some programs but haven't really found what I need. I need a single handed tool wherein,
    A. I can see the exact location (co-ordinates) where my contigs are aligning with respect to the reference genome.
    B. Some of contigs are small but I wish to use them as well. Is there any assembler in which I can select and choose these parameters?
    C. We have also carried some SOLiD sequencing and I need the above program to open and use these reads for aligning sequences as well. (we are thinking to use these reads to fill the gaps/extend the sequences)

    I would really be thankful if anyone helps me out,

    Thanks a ton in advance!

    Kaustubh Gokhale.

  • #2
    So you are aligning the data from those BACs and then assembling the aligned data?

    Try mosaik. It will generate an ace file with all the contigs. You should be able to pull reads from SOLiD too into the assembly.

    Let me know how it goes.


    • #3
      Phrap/ Consed might be able to help you as well.


      • #4
        Mira is a good assembler for multiple types of data. How long are the contigs? You could probably use BLAT


        • #5
          Thank you for suggestions-next problem!

          Hello again and thank you for your suggestions! I shall try to use them and come up with something. Meanwhile I am facing problems with the installation of Mosaik. I have a XP-Home edition system, upon installation, following error code appears,

          'This application has failed to start because application configuration is incorrect.'

          Any help?

          Thanks in advance!

          Kaustubh Gokhale.


          • #6
            I do not know the characteristic of your data. But if you want to align >10kb contigs to a few Gbp genome, my program bwasw (a component of bwa) is the most efficient. Blat is also ok if you only have one BAC. You will find mosaik/ssaha2 too slow for this task.


            • #7
              Thank you 'Ih3'! I've to align 7 individual BACs to ~1.2 Mb reference region! I shall try out bwasw. where can I download it?


              • #8
                At this scale, you do not need bwasw. You may just use blat. If you prefer higher accuracy, try cross_match (it is slower though). If you are interested in bwasw anyway: