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Despite the long history of genome assembly research, there remains a large gap between the theoretical and practical work. There is practical software with little theoretical underpinning of accuracy on one hand and theoretical algorithms which have not been adopted in practice on the other. In this paper we attempt to bridge the gap between theory and practice by showing how the theoretical safe-and-complete framework can be integrated into existing assemblers in order to improve contiguity. The optimal algorithm in this framework, called the omnitig algorithm, has not been used in practice due to its complexity and its lack of robustness to real data. Instead, we pursue a simplified notion of omnitigs (simple omnitigs), giving an efficient algorithm to compute them and demonstrating their safety under certain conditions. We modify two assemblers (wtdbg2 and Flye) by replacing their unitig algorithm with the simple omnitig algorithm. We test our modifications using real HiFi data from the D. melanogaster and the C. elegans genomes. Our modified algorithms lead to a substantial improvement in alignment-based contiguity, with negligible additional computational costs and either no or a small increase in the number of misassemblies. 

A synthetic laser ruby crystal (HD-LR1) is introduced as a new matrix-matched reference material for secondary ionization mass spectrometry (SIMS) analysis of oxygen isotopes in corundum. Laser fluorination isotope ratio mass spectrometry (LF-IRMS) bulk analyses of multiple mg-sized fragments are homogenous, averaging δ18O = +18.40 ± 0.14‰ (95% confidence interval, n = 23) and Δ′17O = −0.368 ± 0.005‰ (as deviation from slope 0.528 for δ′17O vs. δ′18O at 95% conf., n = 11) relative to Vienna Standard Mean Ocean Water (V-SMOW). SIMS spot analyses show homogeneous O-isotopic values at the ng-scale independent of the location in the HD-LR1 single crystal and in four different crystallographic orientations. However, sample surface topography as an artefact of polishing corundum embedded in epoxy creates excess variability in δ18O within ∼100 μm from the edges of the grains. HD-LR1 is a chemical pure crystal with only Cr as a trace component detected at 276 μg g−1 by EPMA, whereas Be, often introduced in artificial gem enhancement, is <0.002 μg g−1 based on SIMS analyses. Therefore, HD-LR1 can also be used as a reference material for Cr, or as a blank for other trace element analyses of corundum by SIMS or LA-ICP-MS.