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
GNU-Parallelimplementation 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.
This release is an incremental update that replaces
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!
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