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 GenoMax, Istvan Albert, and was edited by Istvan Albert,
Letter: We say there is no brain microbiome | New Scientist (www.newscientist.com)
Letter: We say there is no brain microbiome
There is no “brain microbiome” in the sense of a resident microbial community present in the brains of healthy individuals. Instead, microbes enter such sterile tissues through the process of infection. While the role of infections such as Lyme disease in eliciting neurological symptoms may be under-recognised, this is distinct from the idea of a resident microbial community in the brain. Claims of up to 100,000 microbial species per sample in the brain are implausible. Contamination remains the most likely explanation for such findings
Original paper: https://www.newscientist.com/article/mg26335104-500-the-brain-has-its-own-microbiome-heres-what-it-means-for-your-health/
submitted by: Istvan Albert
The brain has its own microbiome. Here's what it means for your health | New Scientist (www.newscientist.com)
Neuroscientists have been surprised to discover that the human brain is teeming with microbes, and we are beginning to suspect they could play a role in neurodegenerative disorders like Alzheimer's
Editor's note: Nick Loman says there is no brain microbiome.
Who should you trust? A popular science magazine that cites neuroscientists making extraordinary claims or someone actually working in microbial bioinformatics? ...
submitted by: Istvan Albert
MassiveFold: unveiling AlphaFold’s hidden potential with optimized and parallelized massive sampling | Nature Computational Science (www.nature.com)
From Abstract: MassiveFold, an optimized and customizable version of AlphaFold that runs predictions in parallel, reducing the computing time from several months to hours. MassiveFold is scalable and able to run on anything from a single computer to a large GPU infrastructure
submitted by: GenoMax
x.com (x.com)
There are 50 petabases of freely-available DNA sequencing data. We introduce "Logan Search" which allows you to search for any DNA sequence in minutes, bringing Earth’s largest genomic resource to your fingertips.
submitted by: Istvan Albert
GitHub - brentp/echtvar: using all the bits for echt rapid variant annotation and filtering (github.com)
Echtvar: Really, truly rapid variant annotation and filtering
Echtvar efficiently encodes variant allele frequency and other information from huge population datasets to enable rapid (1M variants/second) annotation of genetic variants. It chunks the genome into 1<<20 (~1 million) bases, encodes each variant into a 32 bit integer (with a supplemental table for those that can't fit due to large REF and/or ALT alleles). It uses the zip format, delta encoding and integer compression to create a compact and searchable format of any integer, float, or low-cardinality string columns selected from the population file.
submitted by: Istvan Albert
Gapless assembly of complete human and plant chromosomes using only nanopore sequencing (genome.cshlp.org)
we generated ONT Duplex data for three widely studied genomes: human HG002, Solanum lycopersicum Heinz 1706 (tomato), and Zea mays B73 (maize). For the diploid, heterozygous HG002 genome, we also used “Pore-C” chromatin contact mapping to completely phase the haplotypes. We found the accuracy of Duplex data to be similar to HiFi sequencing, but with read lengths tens of kilobases longer, and the Pore-C data to be compatible with existing diploid assembly algorithms. This combination of read length and accuracy enables the construction of a high-quality initial assembly, which can then be further resolved using the UL reads, and finally phased into chromosome-scale haplotypes with Pore-C.
submitted by: Istvan Albert
x.com (x.com)
As strongly requested by the reviewers, here we cite some references [[35], [36], [37], [38], [39], [40], [41], [42], [43], [44], [45], [46], [47]] although they are completely irrelevant to the present work."
https://www.sciencedirect.com/science/article/pii/S0360319924043957
submitted by: Istvan Albert
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