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manta-0.24.0
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@ctsa ctsa released this 09 Jun 23:35
· 1044 commits to master since this release
v0.24.0
72df3da

Extensive runtime optimization and logging to handle several very difficult FFPE cases in practical time.

  • MANTA-213 FFPE runtime optimization:
    • Recognize new BAM record format for fragments shorter than read length, prevent these reads from triggering assembly.
    • Improve insert size distribution estimation by including fragments shorter than read length.
    • Add new runtime instrumentation report for candidate generation
    • Add runtime summary to existing graph report
    • Reduce SW edit matrix size with short k-mer match bounds on ref seq
    • Improve graph noise filtration by testing specific region for evidence signal threshold
    • Use adaptive noise rates in hypoth gen step: background read anomaly rate is used to determine if signal is significant. Currently applies to small assembly candidates only.
    • Collapse redundant assembly candidates for small indels to single copy
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