A simple trimmer that removes sequences from the 3-prime end of Illumina reads. A simple Make workflow has been added to use this tool on multiple FastQ files at once in the workflow directory.
After building the software with the provided Makefile, 2 programs should be created in the bin directory. These 2 binaries are adapter_trim and iupac_trim. The adapter_trim application removes standard sequences from the reads. The iupac_trim program understands the complete IUPAC nucleotide codes.
The adapter trimmer uses a simple match/mismatch scoring algorithm. Reads are trimmed if more than
$match bases match the provided sequence and no more than $mismatch mismatches occurred. Multiple
sequences can be processed at once. No specific paired-end functionality is available in this tool, but
the first and second reads can be processed independantly.
- Implement tests software test. Currently, only a test script with simple test data is present.
Prerequisites:
- BOOST libraries
- BOOST development libraries
cd /path/to/AdapterTrimmer/
make ;