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lecture_notes:04-29-2015 [2015/04/30 23:40]
jennie
lecture_notes:04-29-2015 [2015/04/30 23:41]
jennie
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 ======Team 5 Report: Discovar denovo====== ======Team 5 Report: Discovar denovo======
  
-=====Overview====+=====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.
lecture_notes/04-29-2015.txt ยท Last modified: 2015/04/30 23:45 by jennie