dDocent version 2.0 has arrived with major updates:
- The pipeline now employs a two-step cutoff for data to be included in assembly.
- Assembly accuracy has been improved by replacing the sparse seed clustering of rainbow with alignment based clustering in CD-hit
- dDocent can now natively handle single-end data and paired-end data with substantial overlap between paired reads.
- Parallelization of variant calling has been improved and is now faster with smaller memory loads.
- dDocent can now be run non-interactively by loading a configuration file.