ELAND is the Illumina GA Pipeline proprietary aligner for short read data. I can’t find much documentation on it, and I don’t have the code but this is how I think it basically works, based on reading bits and pieces on the web:


So – quick, but doesn’t (afaIk) take base-call qualities into account, can’t cope with more than 2 mismatches and can only deal with Illumina data (and Illumina length reads). Not sure how ELAND-extended differs. My guess is that the alignment to the first 32 bases is exactly the same, then they do some post-hoc aligning of the extra bits of the sequence?

2 responses to “ELAND

  1. Hi Caroline,
    Can you get additional information from the Illumina website if you have an Illumina user account?

    This is what I got from an Illumina user guide that someone posted on SEQanswers:

    ANALYSIS eland_extended is an improved version of the ANALYSIS eland
    mode. ANALYSIS eland can align reads longer than 32 bases but demands
    that the first 32 bases of the read have a unique best match in the genome.
    The position of this match is used as a “seed” to extend the match along the
    full length of the read. ANALYSIS eland_extended removes the uniqueness
    restriction by considering multiple 32 base matches to be considered and


  2. Ah, ok, thanks! So, the original ELAND aligns as above,and chucks out anything that aligns in multiple places. The extended one does the same thing, but hangs on to multiple matches and then runs a second stage where it looks to see which of the 32b seed alignment positions have the best alignment with the full read length? Presumably it then chucks out anything that *still* matches in multiple places?

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