@jpuritz jpuritz released this Jul 20, 2018 · 13 commits to master since this release

Assets 2

dDocent is now OS X compatible if installed using bioconda

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@jpuritz jpuritz released this Jul 14, 2018 · 20 commits to master since this release

Assets 2

This removes a few outdated dependency checks.

@jpuritz jpuritz released this Jun 26, 2018 · 22 commits to master since this release

Assets 2

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

@jpuritz jpuritz released this Jun 11, 2018 · 34 commits to master since this release

Assets 2

Fixes bug in the configuration file format detection.

@jpuritz jpuritz released this Jun 11, 2018 · 38 commits to master since this release

Assets 2

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

@jpuritz jpuritz released this May 24, 2018 · 152 commits to master since this release

Assets 2

This fixes a bug in interval creation that was introduced in v2.3.4.

@jpuritz jpuritz released this May 22, 2018 · 153 commits to master since this release

Assets 2

This update brings new features to help deal with freebayes instances running out of memory and quitting on certain systems. dDocent now checks for successful completion of each instance, and will rerun with more conservative memory parameters two consecutive times before giving a final error.

This update also includes better code portability, more standardized results from de novo assembly across runs and systems, and more efficient mapping interval creation.

@jpuritz jpuritz released this Jan 8, 2018 · 183 commits to master since this release

Assets 2

Small incremental improvements

@jpuritz jpuritz released this Sep 13, 2017 · 193 commits to master since this release

Assets 2

Fixes version check for BWA

@jpuritz jpuritz released this May 25, 2017 · 195 commits to master since this release

Assets 2

Small bug fixes affecting FASTQ header matching for non-demultiplexed files and fixed CPU limitations for parallel calls.