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lecture_notes:04-29-2015

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lecture_notes:04-29-2015 [2015/04/30 23:41]
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