Skip to content
Fast but inaccurate adapter trimmer for Illumina reads
Branch: master
Clone or download
Permalink
Type Name Latest commit message Commit time
Failed to load latest commit information.
Makefile
README.md typos Jan 12, 2015
illumina.txt
kseq.h
ksw.c make query immutable Dec 20, 2014
ksw.h
kthread.c
test.fa
trimadap-mt.c

README.md

Trimadap is a small tool to trim adapter sequences from Illumina data. It performs SSE2-SW between each read and each adapter sequence and identifies adapter sequences with a few heuristic rules which can be found in the ta_trim1() function in trimadap-mt.c. The default adapters it uses are included in illumina.txt. These are typical Illumina adapters from paired-end sequencing.

Trimadap is designed as an on-the-fly stream filter. It is very fast. In the multi-threading mode, it is as fast as reading through a gzip-compressed FASTQ file. On the other hand, trimadap is very conservative. It is not good in terms of accuracy as of now. I will probably fine tune the heuristic rules in future. This should not be hard in principle, but it takes development time.

You can’t perform that action at this time.