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This edition of the Herald was brought to you by contribution from Istvan Albert, and was edited by Istvan Albert,
A tour de force of ancient DNA analysis | Nature Reviews Genetics (www.nature.com)
The authors carefully assessed the general state of biomolecular preservation using amino acid racemisation, cloned the PCR products to establish whether human contamination had been amplified (it had), and quantified the vanishingly small number of template molecules in the PCR (around 50). Finally, they replicated the assay at an independent lab to eliminate the possibility of lab-specific contamination. By clever primer design, and gradual walking across the mitochondrial genome, it was possible to generate the sequence of the Neanderthal first hypervariable region, totalling 379 base pairs.
submitted by: Istvan Albert
GitHub - CompEpigen/figeno: Tool for plotting sequencing data along genomic coordinates. (github.com)
With figeno, you can plot various types of sequencing data along genomic coordinates. Video overview: .
submitted by: Istvan Albert
Complete sequencing of ape genomes | Nature (www.nature.com)
Here we present haplotype-resolved reference genomes and comparative analyses of six ape species: chimpanzee, bonobo, gorilla, Bornean orangutan, Sumatran orangutan and siamang. We achieve chromosome-level contiguity with substantial sequence accuracy (<1 error in 2.7 megabases) and completely sequence 215 gapless chromosomes telomere-to-telomere. We resolve challenging regions, such as the major histocompatibility complex and immunoglobulin loci, to provide in-depth evolutionary insights.
submitted by: Istvan Albert
K-mer analysis of long-read alignment pileups for structural variant genotyping | Nature Communications (www.nature.com)
Accurately genotyping structural variant (SV) alleles is crucial to genomics research. We present a novel method (kanpig) for genotyping SVs that leverages variant graphs and k-mer vectors to rapidly generate accurate SV genotypes. Benchmarking against the latest SV datasets shows kanpig achieves a single-sample genotyping concordance of 82.1%, significantly outperforming existing tools, which average 66.3%. We explore kanpig’s use for multi-sample projects by testing on 47 genetically diverse samples and find kanpig accurately genotypes complex loci (e.g. SVs neighboring other SVs), and produces higher genotyping concordance than other tools. Kanpig requires only 43 seconds to process a single sample’s 20x long-reads and can be run on PacBio or Oxford Nanopore long-reads.
submitted by: Istvan Albert
GitHub - zeqianli/tgv: Explore genomes in the terminal. Light, blazing fast 🚀, vim-motion. (github.com)
Explore omics data without leaving the terminal.
Light, blazing fast 🚀, vim motion, memory safe.
submitted by: Istvan Albert
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