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  • inchworm and paired ends

    I recently read in the installation README that:

    "There is no 'paired read' mode currently in inchworm. It treats each read independently. If you have pairs, just include them all in a single fasta file with the sequences properly oriented for strand-specificity (sense strand)."

    Does this mean that inchworm does not take insert size information inconsideration when assembling scaffolds?

    Does Butterfly use insert size info to assemble scaffolds?
    Last edited by ians; 10-04-2011, 02:44 PM.

  • #2
    If it said so in the read-me....

    However Butterfly should use read pairs. You might want to download the whole Trinity package and read the manuscript

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    • #3
      ians, imo 'no paired read' mode means the same you infer to me as well = no insert size info.

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      • #4
        Hi ians,

        I think Trinity do accept Paired End Reads as separate files. Please refer to Trinity Manual for more information.

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        • #5
          Thanks for all the feedback!

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