Sequence Condensation Tool - Advanced Settings for Roche/454 Data

NextGENe Online Help : Sequence Condensation Tool : Sequence Condensation Tool - Advanced Settings for Roche/454 Data

For the Roche/454 instrument type, the advanced settings are populated with values that SoftGenetics has determined, from experience, are appropriate for most datasets for the instrument. You can leave these settings as is, or you can modify the settings. At any time, you can click Default Settings to automatically reset all the values to SoftGenetics’s default values.

Setting	Description
Keyword Length [ ] Bases	The minimum length for keywords. The default value is 16 bases.
Long Keyword >= [x] Bases	When a keyword is long because of sequence region without a homopolymer (three or more identical nucleotides), then the keyword can be divided into a smaller size. If the keyword length exceeds the specified value (60 bases is the default value), then it is parsed into multiple keywords at locations with base sequences of AAT or ATT.
Frequency <= [x] Counts and <= [y%] or [z%]	Indicates the count and percentage at which a variation between reads within a single cluster is corrected. If there are less than “x” reads and less than y% of the reads show a variation, then the variation is corrected. If there are more than “x” reads that contain the variation, then the frequency of the variation must be below z% to be corrected.
Combine Both Forward and Reverse	Allows the Error Correction Tool to use reverse complement sequences to calculate variation frequencies. Selecting this option helps to distinguish true SNPs from instrument errors.