Banana Slug Genomics

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=====SGA update=====
  * SGA is a memory efficient assembler
  * It was possible to compute more compressed data
  * The pipeline changed, since it was not easy to figure out how to run it
  * It was necessary to make sure the parameters are running 
  * The group assembled one dataset, merged together
  * SGA indexed each dataset separated
  * Merging is complicated in a pairwise fashion, then two pairs were merged at a time
  * Indexing all three sistinct submissions
  * Pre-processed adapter trimming 
  * Duplicate-removal is later than indexing
  * One issue the group found: SW018 and 19, same library are optical PCR duplicates that should be removed
  * The overall duplication level is a problem
  * Each datset was generated independently
  * Then, removing duplicates should be done apart for each dataset
  * The dataset is very complicated - there is big duplication rate across the dataset the group has
  * Merging indexes - planning on pulling some stats from the grin engine to pull information
  * The wall time is large
  * A variant file with the bubble pop counted the contigs 
  * The group is planning on using the mate-pair data
  * Do adapter removal and index removal - using skewer
  *

Banana Slug Genomics

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