Version 2.5.5

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

Version 2.5.2

Fixes bug in the configuration file format detection.

Version 2.5.1

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

Version 2.3.8 (Important Bug Update)

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

Version 2.3.7

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.

Version 2.2.25

Small incremental improvements

Version 2.2.20

Fixes version check for BWA

2.2.19

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

2.2.16

Fixes some memory issues with Bedtools

2.2.15

Fixes BASH compatibility issues due to GNU-parallel calling a different shell.