Tool to predict primer/adaptor sequences.
Tool will attempt to predict the tag (i.e. primer/adapter) at either or both sites, if possible. The algorithm implemented for the tag prediction assumes the randomness of a typical metagenome. Datasets that do not contain random sequences from organisms in an environment, but rather contain, for example, 16S data may cause incorrect detection of the tag sequences. However, the tag sequences will most likely be over-predicted and can be redefined by the user prior to data processing. The tag sequence prediction uses filtered base frequencies instead of raw base frequencies. This allows a more accurate prediction as it accounts for incomplete and shifted tag sequences. If no tags are reported, then no tags could be identified in the data set.
Input can be a FASTQ file or a FASTA file.
No trimming will be performed.
The output is a tab-delimited text file.
This tool uses the TagCleaner package. Please cite the article:
Schmieder R, Lim YW, Rohwer F, Edwards R, 2010. TagCleaner: Identification and removal of tag sequences from genomic and metagenomic datasets. BMC Bioinformatics. 2010, 11:341.
Please see the TagCleaner homepage for more details.