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Old 04-25-2016, 11:51 PM   #1
Rui Guo
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Default hgap seed seletion step

I want to know how hgap select the seed. The paper says it selects the seed with more than 20x coverage, but doesn't say how it counts the coverage.
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Old 04-26-2016, 08:57 AM   #2
rhall
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The seed will be selected automatically if you input the expected genome size. Coverage is a simply number of bases / genome size.
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Old 04-26-2016, 03:50 PM   #3
Rui Guo
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Do that mean the automatically selected seeds are long enough and has enough coverage? Does it calculate kmer frequency?
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Old 04-26-2016, 06:35 PM   #4
gconcepcion
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Quote:
Originally Posted by Rui Guo View Post
Do that mean the automatically selected seeds are long enough and has enough coverage? Does it calculate kmer frequency?
HGAP is an overlap consensus based assembler and thus no kmer statistics are computed during the assembly process.

As rhall stated, When you set up the run, you input a Genome Size (bp). The algorithm will sort the subreads by length, compute the quantity of bases necessary to obtain appropriate coverage for the Genome Size (bp) that you input during setup and select the longest data necessary to obtain the 30X coverage.

See this for more details:
https://github.com/PacificBioscience...-SMRT-Analysis

Last edited by gconcepcion; 04-26-2016 at 06:36 PM. Reason: because redundancy
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