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Analysis tools to compare two similar Illumina targeted sequencing runs?

What are the commonly used analysis tools to compare two similar targeted sequencing runs done with Illumina?

The type of analysis I am thinking could be useful right now are:

  • Amplification biases
  • Basecalling biases
  • Alignment biases
  • Small variant calling biases
  • SV calling biases
  • Fusion detection biases

By targeted sequencing I mean either amplicon sequencing or pull-down enrichment sequencing protocols, which is the same to say not whole genome sequencing or whole metagenome sequencing runs.

bam analysis targeted
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updated by Ram Ram • written by 14134125465346445 14134125465346445

Presumably you want to look for variants rather than something else. If not, please specify the type of analysis you have in mind.

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updated by Ram Ram • written by Devon Ryan Devon Ryan

Actually I was looking for an answer to this same question, specifically to compare coverage of amplicons between two runs, but the other points listed above would also be useful.

I prepared libraries for 8 samples with two methods of normalization for the same assay. So the amplicons and samples are the same, but we expect the coverage to possibly be different between each set. Is there a tool to compare this? It seems like people took the above question to mean to look for biological differences instead of just a technical comparison.

Thanks!

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written by LindseyKelly • LindseyKelly

Actually.. I have the same question. Did you find the answer?

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written by faramer86 • faramer86

I don't think that just two runs would be sufficient to establish any of that.

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updated by Ram Ram • written by Istvan Albert Istvan Albert

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