SLiMSuite Release v1.12.0 (2024-09-19)

---

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 modephylofas=T to 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=T to 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=INT minimum 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.

BUSCOMP v0.13.0 (MetaEuk) release

BUSCOMP v0.13.0 is now on GitHub. This release features updates to parse additional BUSCO v5 outputs, including transcriptome and proteome mode. It has also been updated to be compatible with MetaEuk runs by generating the missing *.fna files where possible.

The citation remains:

Stuart KC, Edwards RJ, Cheng Y, Warren WC, Burt DW, Sherwin WB, Hofmeister NR, Werner SJ, Ball GF, Bateson M, Brandley MC, Buchanan KL, Cassey P, Clayton DF, De Meyer T, Meddle SL, Rollins LA (preprint): Transcript- and annotation-guided genome assembly of the European starling. bioRxiv 2021.04.07.438753; doi: 10.1101/2021.04.07.438753. [*Joint first authors]

DepthSizer v1.4.0 (IndelRatio) release

DepthSizer v1.4.0 has been released on GitHub. DepthSizer is a program to estimate genome size from an assembly, long-read sequencing data, and BUSCO single-copy orthologue predictions.

DepthSizer works on the principle that Complete BUSCO genes should represent predominantly single copy (diploid read depth) regions along with some poor quality and/or repeat regions. Assembly artefacts and collapsed repeats etc. are predicted to deviate from diploid read depth in an inconsistent manner. Therefore, even if less than half the region is actually diploid coverage, the modal read depth is expected to represent the actual single copy read depth.

This release features an extensive reworking under the hood, which moves the main calculation into R and smooths the read depth modal density calculation. Some of the older, less accurate, approaches have been dropped in favour of some additional mapping adjustments that aim to frame the upper and lower bounds of genome size.

Current citation:

Chen SH, Rossetto M, van der Merwe M, Lu-Irving P, Yap JS, Sauquet H, Bourke G, Bragg JG & Edwards RJ (preprint): Chromosome-level de novo genome assembly of Telopea speciosissima (New South Wales waratah) using long-reads, linked-reads and Hi-C. bioRxiv 2021.06.02.444084; doi: 10.1101/2021.06.02.444084.