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lecture_notes:04-29-2015 [2015/04/29 19:19] chkan |
lecture_notes:04-29-2015 [2015/05/01 06:41] 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. | ||
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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. | ||
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- | </code> |