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sebhtml / ray

Ray -- Parallel genome assemblies for parallel DNA sequencing
http://denovoassembler.sf.net
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compute local coverages during extension to further increase locality #132

Open sebhtml opened 11 years ago

sebhtml commented 11 years ago

Let's say we have a peak coverage of 800 (unique region). Then, during the traversal, it goes down to 300 (unique region), and suddenly, spikes at 600 (repeated region). This will likely cause a misassembly because 600 < 2*800 anyway.

The solution to that is to use an average of the last 512 vertices to compute the value.

sebhtml commented 11 years ago

This ticket may fixes #153 -- it's probably worth a try.

sebhtml commented 11 years ago

Evaluation: 15 human-hours

sebhtml commented 11 years ago

/mnt/lustre03/corbeil/corbeil_group/projects/ray-assembler/tickets/132/contig-13000021

sebhtml commented 11 years ago

distributions

Computing the coverage on seeds is probably good enough.

sebhtml commented 11 years ago

Generating data in /home/boisver1/corbeil_group-lustre03/projects/ray-assembler/tickets/132/ray-ticket-132-2013-06-11-1 for inspection in Ray Cloud Browser.

sebhtml commented 11 years ago

data is in data, will deploy endpoint tomorrow.