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@ekg ekg released this 13 Aug 07:32
· 696 commits to master since this release
v0.1.3
911a28c
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Learn about vigilant mode.
  • Use seeded abPOA mode (in smoothxg). This requires much less memory than the unseeded mode, and allows us to explore much larger POA target lengths (-G).
  • Set a lower POA overlap by default (-O 0.001)
  • Automatically compute smoothxg -w as -G * -n. A specific number of haplotypes can be given via -H, should this differ from -n, in which case the window size is set as -G * -H.

Suggested use: set pggb -k larger than SINE elements or other short repeats in the genome. For human, we use -k 311. A long segment length for mapping is also recommended (in human we use -s 100000). These aren't in the defaults yet, but subsequent releases will have preset settings for different genome lengths and divergences.

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