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  • documentation for ABySS

    Hello,

    I am a new user of ABySS. I have 50 Million Solexa 100bp paired-end transcriptome reads that I am intending to assemble de novo. Velvet could not handle my dataset, but my first run with ABySS worked. However, I have a hard time understanding the output.
    I have 4 questions:

    1) I could not find any documentation on the output files created. Can someone maybe direct me to a page where the various files are explained?

    2) I also do not quite understand if ABySS considers the paired end reads for the alignment or not. Does someone know? I have run the "pe" mode.

    3) What is the number of mismatches allowed in a read to still be assembled to a contig?

    4) below I pasted a few contigs from the outfile that Abyss has created (i.e. xxx_contigs.fa)


    >29036 60 1326
    GGCTCGAGGGTATCTAGAGTCACCAAAGCTGCCGGGCGGGCCCGGGGTGGGTTTGGTCTG
    >29037 61 114
    CGGCTCGAGGGTATCTAGAGTCACCAAAGCTGCCGGGCGGGCCCGGGGTGGGTTTGGGTTG
    >29038 62 268
    TCGGCTCGAGGGTATCTAGAGTCACCAAAGCTGCCGGGCGGGCCCGGGGTGGGTTTGGTGTG
    >29039 60 1139
    GGCTCGAGGGTATCTAGAGTCACCAAAGCTGCCGGGCGGGCCCGGGGTGGGTTTGGGCTG
    >29040 61 51
    CGGCTCGAGGGTATCTAGAGTCACCAAAGCTGCCGGGCGGGCCCGGGGTGGGTTTGGGCCG
    >29041 60 13
    GGCTCGAGGGTATCTAGAGTCACCAAAGCTGCCGGGCGGGCCCGGGGTGGGTTTGGGCTT
    >29042 61 183
    CGGCTCGAGGGTATCTAGAGTCACCAAAGCTGCCGGGCGGGCCCGGGGTGGGTTTGGGGTG
    >29043 61 44
    CGGCTCGAGGGTATCTAGAGTCACCAAAGCTGCCGGGCGGGCCCGGGGTGGGTTTGGTCCG
    >29044 61 70
    CGGCTCGAGGGTATCTAGAGTCACCAAAGCTGCCGGGCGGGCCCGGGGTGGGTTTGGTTTG
    >29045 69 20
    GGCTCGAGGGTATCTAGAGTCACCAAAGCTGCCGGGCGGGCCCGGGGTGGGTTTGGGCTCATAAATGCA
    >29046 69 34
    GGCTCGAGGGTATCTAGAGTCACCAAAGCTGCCGGGCGGGCCCGGGGTGGGTTTGGTCTCATAAATGCA
    >29047 69 20
    GGCTCGAGGGTATCTAGAGTCACCAAAGCTGCCGGGCGGGCCCGGGGTGGGTTTGGTCTTGTAAATGCA

    It is quite clear that these reads are identical with the exception of a few single base mismatchs. Why are they not merged into a single contig?

    Thanks so much for your help!
    Last edited by harrb; 11-23-2010, 08:58 AM.

  • #2
    Originally posted by harrb View Post
    Hello,

    I am a new user of ABySS. I have 50 Million Solexa 100bp paired-end transcriptome reads that I am intending to assemble de novo. Velvet could not handle my dataset, but my first run with ABySS worked. However, I have a hard time understanding the output.
    I have 4 questions:

    1) I could not find any documentation on the output files created. Can someone maybe direct me to a page where the various files are explained?

    2) I also do not quite understand if ABySS considers the paired end reads for the alignment or not. Does someone know? I have run the "pe" mode.

    3) What is the number of mismatches allowed in a read to still be assembled to a contig?

    4) below I pasted a few contigs from the outfile that Abyss has created (i.e. xxx_contigs.fa)


    >29036 60 1326
    GGCTCGAGGGTATCTAGAGTCACCAAAGCTGCCGGGCGGGCCCGGGGTGGGTTTGGTCTG
    >29037 61 114
    CGGCTCGAGGGTATCTAGAGTCACCAAAGCTGCCGGGCGGGCCCGGGGTGGGTTTGGGTTG
    >29038 62 268
    TCGGCTCGAGGGTATCTAGAGTCACCAAAGCTGCCGGGCGGGCCCGGGGTGGGTTTGGTGTG
    >29039 60 1139
    GGCTCGAGGGTATCTAGAGTCACCAAAGCTGCCGGGCGGGCCCGGGGTGGGTTTGGGCTG
    >29040 61 51
    CGGCTCGAGGGTATCTAGAGTCACCAAAGCTGCCGGGCGGGCCCGGGGTGGGTTTGGGCCG
    >29041 60 13
    GGCTCGAGGGTATCTAGAGTCACCAAAGCTGCCGGGCGGGCCCGGGGTGGGTTTGGGCTT
    >29042 61 183
    CGGCTCGAGGGTATCTAGAGTCACCAAAGCTGCCGGGCGGGCCCGGGGTGGGTTTGGGGTG
    >29043 61 44
    CGGCTCGAGGGTATCTAGAGTCACCAAAGCTGCCGGGCGGGCCCGGGGTGGGTTTGGTCCG
    >29044 61 70
    CGGCTCGAGGGTATCTAGAGTCACCAAAGCTGCCGGGCGGGCCCGGGGTGGGTTTGGTTTG
    >29045 69 20
    GGCTCGAGGGTATCTAGAGTCACCAAAGCTGCCGGGCGGGCCCGGGGTGGGTTTGGGCTCATAAATGCA
    >29046 69 34
    GGCTCGAGGGTATCTAGAGTCACCAAAGCTGCCGGGCGGGCCCGGGGTGGGTTTGGTCTCATAAATGCA
    >29047 69 20
    GGCTCGAGGGTATCTAGAGTCACCAAAGCTGCCGGGCGGGCCCGGGGTGGGTTTGGTCTTGTAAATGCA

    It is quite clear that these reads are identical with the exception of a few single base mismatchs. Why are they not merged into a single contig?

    Thanks so much for your help!
    Hi,
    hope this paper may helps you..
    best
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