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lecture_notes:04-29-2015

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lecture_notes:04-29-2015 [2015/04/30 23:44]
jennie
lecture_notes:04-29-2015 [2015/04/30 23:45]
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: 2015/04/30 23:45 by jennie