The current SLiMSuite release is v1.12.0 (2024-09-19) and can be downloaded by clicking the button (left).
In addition to the tarball available via the button (left), SLiMSuite is now available as a GitHub repository (right).
See also: Installation and Setup.
The main updates in SLiMSuite v1.12.0 are:
- Python3. The main tools in use have been updated and checked with Python3. Some older tools might still have bugs.
- BUSCOMP now has a new mode
phylofas=Tto generate output of compiled and renamed files for BUSCO-based phylogenomics. - DepthKopy has undergone several upgrades and will now rate Duplicated BUSCOs (TRUE/FALSE) based on depth, chunk up input for multithreaded processing, and collapse features by depth to estimate total copy number. KAT can now generate the kmer usage in an alternative assembly for comparison.
- DepthSizer has some miscellaneous bug fixes and the same parallisation added to DepthKopy.
- Diploidocus output has been updated for ChromSyn compatibility.
- NUMTFinder has had several coverage and depth bugs fixed.
- PAFScaff has been updated for rapid BUSCO-based mapping. Added
purechrom=Tto enable reciprocal PAFScaff runs for SharpClaw - SynBad has received multiple updates to enable BUSCO mapping and update the assembly map output to be compatible with Telociraptor.
- Telociraptor has received multiple updates to improve generation of tweaked assemblies from assembly maps. It also now features a chromosome sorting and renaming function based on size.
- DepthCharge has a new
minspan=INTminimum spanning bp at end of reads (trims from PAF alignments). - ChromSyn has undergone numerous updates and improvement: see the ChromSyn github for details.
NOTE: Several tools are now maintained and updated more regularly in their own GitHub repos.
