Is there a universal list of 454 and illumina adapters? so that I can trim them using skewer other than its default which misses others. I am working on multiple sequences (454 and illumina) retrieved from SRA.
You can find Illumina adapters in a file included with BBMap suite. It should be in the resources directory of software distribution with name adapters.fa.
454.com is dead so you may need to depend on a third-party source for those adapters. Here is one table and an extended PDF for titanium version.
Thanks @genomax for your great answer. It worked well for illumina sequences but for 454, most of the reads were eliminated after trimming due to size control by skewer (which is 30 bp). should I use the 454 adapters list? or just use the illumina one as they are shorter reads?
If you have adequate amount of Illumina data available then you can set 454 data aside.
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