adapter trimmer

We implement a very simple approach. Each read is searched for the junction adapter (CTGTCTCTTATACACATCT) and its reverse complement (AGATGTGTATAAGAGACAG) based on Hamming distance, the entire junction being CTGTCTCTTATACACATCT+AGATGTGTATAAGAGACAG. If a match to either side of the junction is found then the entire 38bp juncton is clipped. This means the algorithm can tolerate an indel error in one of the sides of the junction, but not both. Optionally Smith-Waterman alignment can be turned on with -w which resolves this issue, although the code is less tested.

eg. this will be caught:

CTGTCTCT-TA-TACACATCTAGATGTGTATAAGAGACAG
but not this:

CTGTCTCT-TA-TACACATCTAGATGT-GTATAAGAGACAG

Project Activity

See All Activity >

Follow adapter trimmer

adapter trimmer Web Site

Other Useful Business Software

Enterprise-grade ITSM, for every business

Give your IT, operations, and business teams the ability to deliver exceptional services—without the complexity.

Freshservice is an intuitive, AI-powered platform that helps IT, operations, and business teams deliver exceptional service without the usual complexity. Automate repetitive tasks, resolve issues faster, and provide seamless support across the organization. From managing incidents and assets to driving smarter decisions, Freshservice makes it easy to stay efficient and scale with confidence.

Try it Free

Rate This Project