feature idea: adapters by platform name

Question

feature idea: adapters by platform name

antonkulaga opened this issue 7 years ago · comments

In the pipelines that deal with GEO it is easy (with GEOParse and other libs) to extract instument_model field from sample descripts with values like "Illumina HiSeq 2000". If users will be able to give such values to atropos instead of manually googling the adapters it would save a lot of time.

Torsten Seemann · Answer 1 · Wed Jul 19 2017 08:30:01 GMT+0800 (China Standard Time)

I can see an adaptor file here:
https://github.com/jdidion/atropos/blob/eddbe9ce3c2b3e835ae42d4c586704da466bc240/atropos/adapters/sequencing_adapters.fa

It's not really instruments @antonkulaga but Platform + Technique, that defines the adaptors.
eg. Nextera + DNA-seq

John Didion · Answer 2 · Tue Oct 10 2017 19:57:29 GMT+0800 (China Standard Time)

I think what you want here will be addressed by the integration of AdapterBase in 1.3. Closing...please reopen if you don't think it will solve your use case.