feature idea: adapters by platform name

jdidion / atropos

An NGS read trimming tool that is specific, sensitive, and speedy. (production)

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feature idea: adapters by platform name #28

Closed antonkulaga closed 7 years ago

antonkulaga commented 7 years ago

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.

tseemann commented 7 years ago

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

jdidion commented 7 years ago

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.