Entering edit mode
5.2 years ago
new15b
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30
Do any of you have experience with either leeHom or Adapterremoval? If you were working with a denovo assembly, would it make more sense to use one or the other for very ancient DNA? As someone very new to bioinformatics, I appreciate the thorough documentation for Adapterremoval, plus I don't have any priori assemblies, so I question whether leeHom would provide any advantages.
If you guys have any tips, I'd greatly appeciate it.
leeHom seems to be specifically designed for ancient DNA where as the other program seems to be a general adapter removal one (there are plenty of others in that category).
You could also look at BBMerge from BBMap suite which can do read merging taking into account errors. You can trim the adapters off as a part of that process or using bbduk afterwards..
I found this paper about Adapterremoval where they claim version 2 is very suitable for ancient DNA: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4751634/
What is your opinion about this?
I will look into BBMerge, thank you!
In that case you may have to try all three tools on your data to see which works best. Sometimes the application depends on data one has.
leeHom has the advantage of computing quality scores accurately for ancient DNA fragments and being the most accurate in terms of sequence length. I recently added to bioconda, let me know if you have problems using it.