Adapter trimming

After sequencing, one of the first steps is to remove adapter sequences. These are most commonly the sequences that are either used to initiate sequencing like a universal primer, or are barcoding sequences for multiplexing.

Since these are artificial sequences, we try to remove them using software like trimmomatic or cutadapt. However, when I looked at the software for either of these, I was mildly shocked that the adapter sequences were either hard coded, in the software repo but not standalone, or just not present at all. I decided to make a place to store just the adapter sequences, so that future versions of these packages or future software can just access the sequences. Check it out here: https://github.com/lskatz/adapterseqs.

I could not find a single repo with all sequences and so I just made it easy on myself in making it:

1) I took all sequences found in the Trimmomatic repo and copied them over with the Illumina copywrite. 2) I parsed the Porechop repo, or rather a fork of it from Sam Wilkinson, and saved it as a fasta file ¹. 3) I added an open source license so that it is actually usable by anybody. 4) I added unit tests to the repo to make sure that other software can use the adapters.

I also took the extra step in adding a simple adapter trimming method in fasten_trim.

1. Showing my work: cat adapters.py | perl -lane 'if(/(start_sequence|end_sequence)=\((\S+),\s+(\S+?)\)+/){$id=$2; $dna=$3; print ">$id\n$dna";} ' | perl -plane "s/'//g" > Porechop.fa ↩