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lecture_notes:05-15-2015 [2015/05/18 14:48] gepoliano |
lecture_notes:05-15-2015 [2015/05/18 15:02] gepoliano |
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=====SGA update===== | =====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 |