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  • Velvet 1.2.10 with FASTQs of different read-lengths AND paired- and single-end?

    Greetings.

    I have been using Velvet 1.2.10 to create de novo assembled contigs with good results using 100bp paired-end reads.

    Now I have more and different data, because I have longer reads and because I now trim for quality using Btrim64. As a result, from the two original sets of paired-end reads, 100 and 250bp reads (with 400 and 600 bp insert sizes, respective) I have 4 sets of reads:

    Sample1_100bp_R1.fastq.pe
    Sample1_100bp_R2.fastq.pe
    Sample1_100bp_R1.fastq.se
    Sample1_100bp_R2.fastq.se
    Sample1_250bp_R1.fastq.pe
    Sample1_250bp_R1.fastq.pe
    Sample1_250bp_R2.fastq.pe
    Sample1_250bp_R1.fastq.se
    Sample1_250bp_R2.fastq.se

    (The single reads result when the pair is sacrificed in the quality trimming)

    I have 3 questions:

    Is it possible to combine all of these data for a de novo assembly in Velvet?

    Are the 250bp reads still considered short reads or are they long reads?

    Is there a problem now that the read-length is no longer consistent due to trimming?

    Thanks!

  • #2
    Originally posted by Genomics101 View Post

    Is it possible to combine all of these data for a de novo assembly in Velvet?
    Yes. You may have to recompile velvet to run with a larger number of categories, probably 'CATEGORIES=4' .
    You should flag your 2 sets of PE reads as -shortPaired and -shortPaired2, respectively.

    Originally posted by Genomics101 View Post

    Are the 250bp reads still considered short reads or are they long reads?
    See the discussion about this in the velvet manual,



    I think it's probably up to you whether you want to consider them long reads or short reads.

    see also this thread in the Velvet mailing list archives:



    Originally posted by Genomics101 View Post

    Is there a problem now that the read-length is no longer consistent due to trimming?
    No.
    Last edited by mastal; 12-31-2013, 04:18 AM.

    Comment


    • #3
      Thanks very much, the Manual for my version of Velvet was unclear about all these points and I very much appreciate your time on this.

      Comment

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