The Biostar Herald publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed. You too can submit links here.
This edition of the Herald was brought to you by contribution from Istvan Albert, Dave Carlson, and was edited by Istvan Albert,
GitHub - ksahlin/strobealign: Aligns short reads using dynamic seed size with strobemers (github.com)
Strobealign is a read mapper that is typically significantly faster than other read mappers while achieving comparable or better accuracy, see the performance evaluation.
Strobealign v0.15.0 is released: (1) Allows more indexed contigs (2^32), (2) adds a mode --mcs which increase accuracy
Paper on mcs : https://www.biorxiv.org/content/10.1101/2024.10.29.620855v1
submitted by: Istvan Albert
ganon2 (pirovc.github.io)
ganonis designed to index large sets of genomic reference sequences and to classify reads against them efficiently. The tool uses Hierarchical Interleaved Bloom Filters as indices based on k-mers with optional minimizers. It was mainly developed, but not limited, to the metagenomics classification problem: quickly assign sequence fragments to their closest reference among thousands of references. After classification, taxonomic or sequence abundances are estimated and reported.
submitted by: Istvan Albert
Genomic analyses of hair from Ludwig van Beethoven (www.cell.com)
- Eight locks of hair attributed to Ludwig van Beethoven underwent genomic analyses
- We deemed five of these authentic and sequenced Beethoven’s genome to high coverage
- Beethoven had a predisposition for liver disease and became infected with hepatitis B
- We also discovered an extra-pair-paternity event in Beethoven’s paternal line
submitted by: Istvan Albert
Notes from Beethoven's genome00025-3) (www.cell.com)
In a recent notable study, Begg et al.1 used Ludwig van Beethoven’s hair strands for genome sequencing and explored genetic predispositions for some of his documented medical issues. Given that it was arguably Beethoven’s skills as a musician and composer that made him an iconic figure in Western culture, we here extend the approach and apply it to musicality.
Beethoven’s PGI for beat synchronization places him in the 9th percentile for STAGE (Figure 1A) and the 11th percentile for BioVU (Figure 1B), indicating a relatively low PGI compared with both reference cohorts. Comparison of Beethoven’s data with the cohorts’ principal components (Figure S1E,F) suggests that the results are unlikely to be influenced by ancestry differences.
submitted by: Istvan Albert
CGC1, a new reference genome for Caenorhabditis elegans | bioRxiv (www.biorxiv.org)
Here we provide a 106.4 Mb gap-free, telomere-to-telomere genome assembly of C. elegans, generated from CGC1, an isogenic derivative of the N2 strain. We used improved long-read sequencing and manual assembly of 43 recalcitrant genomic regions to overcome deficiencies of prior N2 and VC2010 assemblies, and to assemble tandem repeat loci including a 772-kb sequence for the 45S rRNA genes. While many differences from earlier assemblies came from repeat regions, unique additions to the genome were also found. Of 19,972 protein-coding genes in the N2 assembly, 19,790 (99.1%) encode products that are unchanged in the CGC1 assembly. The CGC1 assembly also may encode 183 new protein-coding and 163 new ncRNA genes.
submitted by: Istvan Albert
When less is more: sketching with minimizers in genomics | Genome Biology | Full Text (doi.org)
Recent review paper explaining what genomic minimizers are what they are used for.
submitted by: Dave Carlson
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