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, manaswwm, and was edited by Ram, Istvan Albert,
Journal of Open Source Software: Mashtree: a rapid comparison of whole genome sequence files (joss.theoj.org)
Min-hash creates distances between any two genomes, min-hash values can be used to rapidly cluster genomes into trees using the neighbor-joining algorithm (Saitou & Nei, 1987). We implemented this idea in software called Mashtree, which quickly and efficiently generates large trees that would be too computationally intensive using other methods.
submitted by: Istvan Albert
GitHub - vanheeringen-lab/genomepy: genes and genomes at your fingertips (github.com)
genomepy is designed to provide a simple and straightforward way to download and use genomic data. This includes (1) searching available data, (2) showing the available metadata, (3) automatically downloading, preprocessing and matching data and (4) generating optional aligner indexes. All with sensible, yet controllable defaults. Currently, genomepy supports Ensembl, UCSC, NCBI and GENCODE.
submitted by: Istvan Albert
I think we need to talk about how devastating this cancer microbiome refutation paper from@StevenSalzberg1
and colleagues is. It really speaks to how devoid of critical thinking and intellectual depth our glam publishing ecosystem has become. 1/nhttps://t.co/wWsHTa4K8x
— Professor Booty PhD (@ProfBootyPhD) August 7, 2023
I think we need to talk about how devastating this cancer microbiome refutation paper from@StevenSalzberg1
and colleagues is. It really speaks to how devoid of critical thinking and intellectual depth our glam publishing ecosystem has become. 1/nhttps://t.co/wWsHTa4K8x
submitted by: Istvan Albert
Challenges in identifying mRNA transcript starts and ends from long-read sequencing data | bioRxiv (www.biorxiv.org)
Here, we systematically assess the variability and accuracy of mRNA terminal ends identified by LRS reads across multiple sequencing platforms. We find substantial inconsistencies in both the start and end coordinates of LRS reads spanning a gene, such that LRS reads often fail to accurately recapitulate annotated or empirically derived terminal ends of mRNA molecules.
submitted by: Istvan Albert
Evolution of a minimal cell | Nature (www.nature.com)
Evolution of a minimal version of a bacterial cell
submitted by: manaswwm
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