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I have a set of experiments which should result in WGS reads with a high density of indels.

Question: Are there certain alignment tools/methods which perform respectively "better" with these reads? I'm not very interested in performance, but rather "better" in terms of dealing with the presence of many deletions/insertions.

Options I know of:

  • BWA (I think there are special settings whereby I could run bwa for this case, e.g. see this)

  • BBMap

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  • $\begingroup$ try Stampy? ... $\endgroup$ Mar 20 '18 at 19:15
  • $\begingroup$ @Chris_Rands Have you seen this benchmarked against the others? $\endgroup$
    – EB2127
    Mar 20 '18 at 20:30
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    $\begingroup$ Which platform do you use? The link about bwa mem is about ONT platform. And what kind of indels are you talking about, small ones? $\endgroup$
    – benn
    Mar 21 '18 at 11:04
  • $\begingroup$ @b.nota Small indels, but a high density of these small indels $\endgroup$
    – EB2127
    Mar 22 '18 at 3:50
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Minimap2 attempts to solve a lot of problems that are not properly dealt with by other mapping software. It's written by the same author as BWA, but designed to deal with situations where the reference and query sequences are quite different (e.g. for noisy long reads).

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  • $\begingroup$ This is a great point, thanks! I've heard good things about this with PacBio reads $\endgroup$
    – EB2127
    Mar 22 '18 at 3:50
  • $\begingroup$ I will also keep this question open for a few more days; this is a great answer though! $\endgroup$
    – EB2127
    Mar 22 '18 at 16:35

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