Base quality normally drops towards the end of a read hence, trimming low quality ends of sequences is advisable before assembling a contig.
To trim low quality ends you will have to configure the options as required.
- Annotate new trimmed regions - This calculates new trimmed regions and annotate them as trimmed. The trimmed regions will be ignored when performing assembly and calculating the consensus sequence.
- Remove new trimmed regions from sequences - This calculates new trimmed regions and remove them from the sequence(s) completely.
- Remove existing trimmed regions from sequences - This will remove the existing trimmed regions from the sequences permanently; no new trimmed regions are calculated.
- Trim vectors - Screens the sequences against UniVec to locate any vector contamination and trim it. This uses an implementation similar to NCBI’s VecScreen to detect contamination (http://www.ncbi.nlm.nih.gov/projects/ VecScreen/).
- Error Probability Limit - Available for chromatogram documents which have quality (confidence) values. The ends are trimmed using the modified-Mott algorithm (see below) based on these quality values (Richard Mott personal communication).
- Maximum low quality bases - Specifies the maximum number of low quality bases that can be in the untrimmed region. Low Quality is normally defined as confidence of 20 or less. This can be adjusted on the Sequencing and Assembly tab of Preferences.
- Maximum Ambiguities - Finds the longest region in the sequence with no more N’s than the maximum ambiguous bases value and trims what is not in this region. This should be used when sequences have no quality information attached.
- Trim 5’ End and Trim 3’ End - These can be set to specify trimming of only the 3’ or 5’ end of the sequence. A minimum amount that must be trimmed from each end can also be specified.
- Maximum length after trim - If the untrimmed region is longer than the specified limit then the remainder will be trimmed from the 3’ end of the sequence until it is this length.
Note that we currently only support UniVec databases. If you would like to use custom BLAST databases to trim vector sequences, please contact our support team.