cnobles / seqtrimr Goto Github PK

If the boundary sequences are known, and the paired-read has been trimmed on it's 5' or leading side, then an alignment of the paired reads should show precisely where the overreading sequence starts. If there is no overreading section, then the reads don't have enough sequence length to overread and then it's not a problem. The problem with this idea so far is the processing time. Need to find an efficient means of pairwiseAlignment between the reads.

Add features to trim initially based on sequence quality for N number of sequential bases. This could be implemented prior to nucleotide matching for fastq files.