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lecture_notes:04-29-2015 [2015/04/29 19:19] chkan |
lecture_notes:04-29-2015 [2015/05/01 06:45] (current) 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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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: | + | |
- | Spri beads size selection. | + | |
- | No amplification in adapter phase. | + | |
- | Wants a single library on an illumia machine. | + | |
- | Different Error Correction/Gap filling steps: | + | =====Before assembly===== |
- | Use sequential error correction increasing in difficulty to reduce computation | + | * Spri beads size selection. |
- | Look for isolated loser calls which means no LQ scores adjacent and corrects the scores up. | + | * No amplification in adapter phase. |
- | Reduce quality scores in a sliding window. Correct artifically high quality scores with adjacent low scores | + | * Wants a single library on an illumia machine. |
- | Assembly: | + | =====Different error correction/gap filling steps===== |
- | Use the good founder pairs from previous steps to "seed" building the genome. | + | * 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. | ||
+ | * Reduce quality scores in a sliding window. Correct artifically high quality scores with adjacent low scores | ||
- | </code> | + | =====Assembly===== |
+ | * Use the good founder pairs from previous steps to "seed" building the genome. |