Banana Slug Genomics

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======Team 5 Report: Discovar denovo======

=====Overview=====
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. 
Most of the information is the in the PPT here. The notes below are supplemental.

Basic Outline:
  * Builds stacks
  * Filters out crap
  * Builds consensus
  * Trys to merge stacks
  * Using pairwise windows. If it finds a match it checks adjacent windows for overlap before they link them
  * Correct paired ends against each other
  * 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=====
  * 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

=====Assembly=====
  * Use the good founder pairs from previous steps to "seed" building the genome.

Banana Slug Genomics

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