SLiMSuite v1.9 sees the introduction of four genome assembly tools:
- Diploidocus = Diploid genome assembly analysis toolkit. Includes assembly cleanup (haplotig/artefact removal), genome size prediction and read depth copy number analysis.
- PAFScaff = Pairwise mApping Format reference-based scaffold anchoring and super-scaffolding. Uses minimap2 to map a genome assembly onto reference chromosomes.
- SAAGA = Summarise, Annotate & Assess Genome Annotations. Uses a reference proteome to summarise and assess genome annotations.
- SynBad = Synteny-based scaffolding adjustment tool for comparing two related genome assemblies and identify putative translocations and inversions between the two that correspond to gap positions. (Development only.)
There have also been significant updates to:
- BUSCOMP = BUSCO Compiler and Comparison tool. Used for genome assembly completeness estimates that are robust to sequence quality, and for compiling BUSCO results.
Other changes include some initial reformatting for Python3 compatibility. This is ongoing work; please report any odd behaviour.
See the included release_notes.txt for a full list of the python module updates since v1.8.1.