| | 5-Step Computational Pipeline for INDEL identification |
| | 1. Vector screening using NCBI VecScreen system and trimming based on quality score. |
| | Traces are trimmed when scores are below 25 for 5 bases in a row. |
| | Moreover, trimmed length has to be at least 100 bases with average score equal or above 25. |
| | 2. Repeatmask traces |
| | 3. Megablast to Goldenpath with these options "-q -100 -p 95 -F F" |
| | 4. For each trace that hits Goldenpath, identifying anchor sequence with a minimum of 50 bases |
| | and 100% match to a single location. Based on the anchor sequences, traces are then unmasked |
| | and aligned against the mapped locations using bl2seq. |
| | 5. INDELS that are surrounded by 5 neighboring bases with minimum score of 25 are recorded. |
| | PARAMETER:NA |
