lecture_notes:04-29-2015
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lecture_notes:04-29-2015 [2015/04/29 19:19] chkan |
lecture_notes:04-29-2015 [2015/05/01 06:40] jennie |
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| - | <code> | + | ======Team 5 Report: Discovar denovo====== |
| + | |||
| + | =====Overview==== | ||
| Discovar denovo is by the Broad institute. It is a total pipeline, meaning that one needs to follow | Discovar denovo is by the Broad institute. It is a total pipeline, meaning that one needs to follow | ||
| the sequencing as well as assembly protocols to obtain the best results. | the sequencing as well as assembly protocols to obtain the best results. | ||
| Line 13: | Line 15: | ||
| 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. | ||
| - | |||
| - | </code> | ||
lecture_notes/04-29-2015.txt · Last modified: 2015/05/01 06:45 by jennie
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