lecture_notes:04-29-2015
Differences
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lecture_notes:04-29-2015 [2015/05/01 06:41] jennie |
lecture_notes:04-29-2015 [2015/05/01 06:44] jennie |
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| Basic Outline: | Basic Outline: | ||
| - | Builds stacks | + | * Builds stacks |
| - | Filters out crap | + | * Filters out crap |
| - | Builds consensus | + | * Builds consensus |
| - | Trys to merge stacks | + | * Trys to merge stacks |
| - | Using pairwise windows. If it finds a match it checks adjacent windows for overlap before they link them | + | * Using pairwise windows. If it finds a match it checks adjacent windows for overlap before they link them |
| - | Correct paired ends against each other | + | * Correct paired ends against each other |
| - | Then build using HQ pairs | + | * Then build using HQ pairs |
| =====Before assembly===== | =====Before assembly===== | ||
| - | Spri beads size selection. | + | * Spri beads size selection. |
| - | No amplification in adapter phase. | + | * No amplification in adapter phase. |
| - | Wants a single library on an illumia machine. | + | * Wants a single library on an illumia machine. |
| =====Different error correction/gap filling steps===== | =====Different error correction/gap filling steps===== | ||
| - | Use sequential error correction increasing in difficulty to reduce computation | + | * Use sequential error correction increasing in difficulty to reduce computation |
| - | Look for isolated loser calls which means no LQ scores adjacent and corrects the scores up. | + | * Look for isolated loser calls which means no LQ scores adjacent and corrects the scores up. |
| - | Reduce quality scores in a sliding window. Correct artifically high quality scores with adjacent low scores | + | * Reduce quality scores in a sliding window. Correct artifically high quality scores with adjacent low scores |
| =====Assembly===== | =====Assembly===== | ||
| - | Use the good founder pairs from previous steps to "seed" building the genome. | + | * Use the good founder pairs from previous steps to "seed" building the genome. |
lecture_notes/04-29-2015.txt · Last modified: 2015/05/01 06:45 by jennie
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