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Khabre desk
Recent reporting, analysis and explainers from the Genomics desk.
science
A bioRxiv preprint describes DeepMM, a method that detects suspected misassembly junctions and splits contigs before microbial genomes are grouped into bins. In benchmark datasets, this reduced gene annotations that disagreed with sample-matched reference genomes.
science
A bioRxiv preprint reports that oversampling closely related prokaryotic strains makes genome collections less informative than their raw counts suggest. Applying the authors’ PhyloThin method to 402 species, the study estimates that the effective sample count is 41% below the actual count.
science
A bioRxiv preprint presents LongPhase-TO, a long-read method for reconstructing somatic haplotypes from tumour samples without matched normal DNA. In tests on eight datasets from six cancer cell lines, the method lengthened haplotype blocks and improved somatic variant-calling scores.
science
A University of Michigan team has introduced AmbientMapper, a computational method that estimates ambient chromatin contamination in combinatorial single-cell experiments. In a bioRxiv preprint, the authors report a 0.19% wrong-genome rate on a 26-genome reference panel and recovery of low-depth nuclei that standard pipelines discarded.
science
A bioRxiv preprint presents PHACTn, a training-free method that uses mammalian evolutionary history to infer how tolerable single-nucleotide variants may be across the human genome. The authors report strong performance on benchmark sets of non-coding variants using four interpretable parameters and no GPU.
science
Google DeepMind says AlphaGenome Atlas pre-calculates predicted molecular effects for approximately 9 billion possible single-nucleotide changes, giving researchers a searchable tool for prioritising variants.
science
Google DeepMind says AlphaGenome Atlas precomputes molecular-effect predictions for approximately 9 billion single-nucleotide variants and provides scores and interpretation tools for non-commercial academic research.