Herald:The Biostar Herald for Tuesday, May 23, 2023
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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, and was edited by Istvan Albert,


A mental-health crisis is gripping science — toxic research culture is to blame (www.nature.com)

There is a mental-health crisis in science — at all career stages and across the world. Graduate students are being harassed and discriminated against, paid meagre wages, bullied, overworked and sometimes sexually assaulted. It doesn’t get much better for early-career researchers struggling to land long-term employment. And established senior researchers face immense pressure to win grants, publish in high-profile journals and maintain their reputations in highly competitive fields.

submitted by: Istvan Albert


Linear time complexity de novo long read genome assembly with GoldRush | Nature Communications (www.nature.com)

Current state-of-the-art de novo long read genome assemblers follow the Overlap-Layout-Consensus paradigm. While read-to-read overlap – its most costly step – was improved in modern long read genome assemblers, these tools still often require excessive RAM when assembling a typical human dataset. Our work departs from this paradigm, foregoing all-vs-all sequence alignments in favor of a dynamic data structure implemented in GoldRush, a de novo long read genome assembly algorithm with linear time complexity.

submitted by: Istvan Albert


https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkad382/7167344

PHASTEST (PHAge Search Tool with Enhanced Sequence Translation) is the successor to the PHAST and PHASTER prophage finding web servers. PHASTEST is designed to support the rapid identification, annotation and visualization of prophage sequences within bacterial genomes and plasmids. PHASTEST also supports rapid annotation and interactive visualization of all other genes (protein coding regions, tRNA/tmRNA/rRNA sequences) in bacterial genomes.

submitted by: Istvan Albert


submitted by: Istvan Albert


Reconstruction of the personal information from human genome reads in gut metagenome sequencing data | Nature Microbiology (www.nature.com)

Here we used genomic approaches to reconstruct personal information from the faecal metagenomes of 343 Japanese individuals with associated human genotype data. Genetic sex could be accurately predicted based on the sequencing depth of sex chromosomes for 97.3% of the samples. Individuals could be re-identified from the matched genotype data based on human reads recovered from the faecal metagenomic data with 93.3% sensitivity using a likelihood score-based method. This method also enabled us to predict the ancestries of 98.3% of the samples.

submitted by: Istvan Albert


Bioconductor - fluentGenomics (development version) (bioconductor.org)

An extended workflow using the plyranges and tximeta packages for fluent genomic data analysis. Use tximeta to correctly import RNA-seq transcript quantifications and summarize them to gene counts for downstream analysis. Use plyranges for clearly expressing operations over genomic coordinates and to combine results from differential expression and differential accessibility analyses.

submitted by: Istvan Albert


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