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 06:45] (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. | ||
| Line 5: | Line 7: | ||
| 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. | ||
lecture_notes/04-29-2015.1430335175.txt.gz · Last modified: 2015/04/29 19:19 by chkan
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