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This fairly large update include the following improvements:
dDocentis 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.shcan now take a range of similarity values as input
- Multiple minor bug squashes
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.