Pluribus
Running PluribusFast
Usage: java -jar Pluribusfast.jar <Start Level> <Validation Chars> <Cutoff> <Input> <Output>
Example: java -jar PluribusFast.jar 20 4 3 UncorrectedReads.fa CorrectedReads.fa
PluribusFast Parameters
- Start Level - The first level of the suffix trie to construct / shortest substring stored (Recommended value 20)
- Validation Chars - Numbers of characters used to validate candidate corrections (Recommended value 4)
- Cutoff - Threshold for high frequency substrings (Recommended value 3, but for coverage <30 use 2)
- Input - Data to be corrected by PluribusFast
- Output - Where PluribusFast will write the corrected reads
Running Pluribus
Here are descriptions of the different parameters for Pluribus
- J - The first level of the suffix tree to construct (Recommended value ~20)
- K - The last level of the suffix tree to construct (Recommended value J + 4 or ~24)
- I - Number of levels of the tree to pull candidate corrections from (Optional, though required if V is specified)
- V - Minimum number of matching characters in the tail after a correction (Optional, though required if I is specified)
- Cutoff - Threshold for High Frequency (Recommended value = 2)
- NumSuffix - Minimum number of votes required to make a correction (Recommended value = 1)
- SubOnly - Only allow substitution type corrections to be applied (Such as correcting Illumina data)
- ErrorData - Data to be corrected
- CorrectedDataOutput - Where the corrected data will be written to
