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chapmanb / bcbb

Incubator for useful bioinformatics code, primarily in Python and R
http://bcbio.wordpress.com
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adaptor_trim.py #84

Closed radaniba closed 10 years ago

radaniba commented 10 years ago

Hi Brad,

I am running a test of your code for adaptor trimming (http://coderscrowd.com/app/codes/view/224), the unit test is Ok. I don't see though why this code would not work for long reads. In the description of the code you mentioned that the code is designed for short read sequencing, can you please enlighten me on this ?

Thanks

Rad

chapmanb commented 10 years ago

Rad; I can't access the example you're describing but if the code is useful as an example that's great. It's multiple years out of date now and will be slow and inefficient so is not suited for use in real life work. It will work fine on any size read but won't scale well.

If you want something production level, a tool like AlienTrimmer (http://www.ncbi.nlm.nih.gov/pubmed/23912058), Cutadapt (http://code.google.com/p/cutadapt/) or Scythe (https://github.com/vsbuffalo/scythe) are better suggestions.

Thanks much and hope this helps.

radaniba commented 10 years ago

Hi Brad,

Thanks a lot for these recommendations

Rad