- Contigs are now named in a reproducible manner, i.e. if assembly is rerun with the same inputs/parameters, the output should be identical
- Removed BioPerl dependencies to facilitate installation at external sites
- Fixed the bug where merblast output was being deleted prematurely with -cleanup_level 2
- Fixed the bug in merBlast where not all contig-splinting alignmens were reported
- Fixed the bug in the ordering of the threaded merblast outputs
- Disabled the logic to determine the number of chunks to split the fastqs based on num_local_procs if not using cluster. It limited user to that number of chunks even if they switch to another machine or cluster later.
- Added auto-detection of the bubble_depth_cutoff. Users no longer need to stop in the middle of a diploid run to determine it. Manual setting is still supported and will turn off auto-detect
- Scaffolding now uses both splinting and spanning reads in the same round. The two types can add complimentary information and as a result reduce misjoins.
- Inside scaffolds, contig ends are trimmed back if the *estimated* gap size between them is less than 10bp. This is done to avoid overlapping redundant ends.
- Added a helper script boostrap_run.sh that allows creating a pseudo-run structure based on another run up to a specified stage. User can then create a new “branch” by running meraculous.pl with the -resume and -dir options pointing to the new run structure. This allows creating multiple assembly versions that have common initial stages (e.g. different scaffolding settings starting with the same UUtigs)