Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • 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
    Attached Files

    Comment

    Latest Articles

    Collapse

    • seqadmin
      Strategies for Sequencing Challenging Samples
      by seqadmin


      Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
      03-22-2024, 06:39 AM
    • seqadmin
      Techniques and Challenges in Conservation Genomics
      by seqadmin



      The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

      Avian Conservation
      Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
      03-08-2024, 10:41 AM

    ad_right_rmr

    Collapse

    News

    Collapse

    Topics Statistics Last Post
    Started by seqadmin, 03-27-2024, 06:37 PM
    0 responses
    12 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 03-27-2024, 06:07 PM
    0 responses
    11 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 03-22-2024, 10:03 AM
    0 responses
    53 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 03-21-2024, 07:32 AM
    0 responses
    69 views
    0 likes
    Last Post seqadmin  
    Working...
    X