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@jpuritz jpuritz released this Feb 12, 2021 · 1 commit to master since this release

fixes #71 which resulted in an inefficient scan of the reference genome to determine if created by dDocent.

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@jpuritz jpuritz released this Feb 12, 2021 · 2 commits to master since this release

This version bring minor bug fixes and several improvements:

  • Better and more even memory management for genotyping
  • Sorted reference sequences
  • Bug fix in PE assembly responsible for a small percentage of misassembled loci when F and PE reads overlapped.
  • The deprecation of the MAXMemory option. The GNU-Parallel implementation does not actually limit memory usage and can cause failed genotyping instances. The better memory management strategy implemented in this update should alleviate major memory issues.
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@jpuritz jpuritz released this May 2, 2019 · 69 commits to master since this release

Update remake_reference.sh script and add version to logfiles

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@jpuritz jpuritz released this Mar 7, 2019 · 71 commits to master since this release

Fixes small bug if assembling data with less than 8 processors.

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@jpuritz jpuritz released this Feb 28, 2019 · 72 commits to master since this release

This release is an incremental update that replaces trimmomatic with fastp for quality and adapter trimming. fastp is faster, does not rely on a java Environment, and can automatically detect adapters without relying on a list (that also must be installed).

Read trimming is now much faster, and the dDocent environment and dependency list is lighter!

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@jpuritz jpuritz released this Jul 20, 2018 · 98 commits to master since this release

dDocent is now OS X compatible if installed using bioconda

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@jpuritz jpuritz released this Jul 14, 2018 · 105 commits to master since this release

This removes a few outdated dependency checks.

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@jpuritz jpuritz released this Jun 26, 2018 · 107 commits to master since this release

This update is largely internal changes to speed up performance and to increase code portability.

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@jpuritz jpuritz released this Jun 11, 2018 · 119 commits to master since this release

Fixes bug in the configuration file format detection.

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@jpuritz jpuritz released this Jun 11, 2018 · 123 commits to master since this release

This fairly large update include the following improvements:

  • dDocent is now far more accurate when assembling loci from paired-end data generated from the original RAD protocol
  • All versions of assembly are now faster and more efficient
  • Assembly cutoff values can now be entered in the configuration file. See Configuration Example for the correct formatting
  • Progress Bar has now been added for SNP calling
  • SNP calling restarts because of memory limits are now more incremental
  • Maximum memory limits should behave more appropriately
  • Terminal outputs have been cleaned up and simplified
  • The optimization script ReferenceOpt.sh can now take a range of similarity values as input
  • Multiple minor bug squashes
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