Monday 11 October 2021

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.