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  • Assembling against a reference

    Hello everyone,

    I have been doing some reading about mapping and assembling against a reference and I cannot quite understand the difference? What I understand it that mapping against a reference gives alignment scores while assembling produce a set of contigs.

    I have used CLCworkbench - maps reads against a reference, runMapping from Newbler and MIra to do a mapping assembly? I get a list of contigs as well.

    Some sources say that mapping is not assembly. Can anyone please explain to me or give me some papers to understand this please.

    Thank you.

  • #2
    This should help.

    Transcriptomics studies often rely on partial reference transcriptomes that fail to capture the full catalogue of transcripts and their variations. Recent advances in sequencing technologies and assembly algorithms have facilitated the reconstruction of the entire transcriptome by deep RNA sequencin …

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