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, aswathyseb, and was edited by Istvan Albert,
Michael Eisen on Twitter (x.com)
Here's the thing. We have NO IDEA how to pick good graduate students. I served on admission committees for 10+ years, and chaired a few, and what I learned is that all the spreadsheets of grades and test scores and recommendations and essays and publications and interview rubrics are just an elaborate ruse to pretend we know what we're doing when we simply don't. Many of the most highly ranked applicants to our "top" program flamed out quickly, and tons of the students we summarily rejected have turned into amazing scientists. But in the name of creating meritocratic seeming rankings that are more about creating a workforce than great scientists (a system that anyone paying attention knows is bullshit), we've created a homogenous process adopted by nearly all institutions that has stamped out the one thing we should be striving for - given our lack of any clear understanding of what leads to success - a wide range of difference talents and experiences.
submitted by: Istvan Albert
TreeWave: command line tool for alignment-free phylogeny reconstruction based on graphical representation of DNA sequences and genomic signal processing | BMC Bioinformatics | Full Text (doi.org)
TreeWave: command line tool for alignment-free phylogeny reconstruction based on graphical representation of DNA sequences and genomic signal processing
submitted by: aswathyseb
mulea: An R package for enrichment analysis using multiple ontologies and empirical false discovery rate | BMC Bioinformatics | Full Text (bmcbioinformatics.biomedcentral.com)
mulea: An R package for enrichment analysis using multiple ontologies and empirical false discovery rate
submitted by: aswathyseb
NextPolish2: A Repeat-aware Polishing Tool for Genomes Assembled Using HiFi Long Reads (doi.org)
NextPolish2: A Repeat-aware Polishing Tool for Genomes Assembled Using HiFi Long Reads
submitted by: aswathyseb
GitHub - rrwick/Autocycler: A tool for generating consensus long-read assemblies for bacterial genomes (github.com)
New year, new assemblies! Autocycler, a new tool for consensus assembly of long-read bacterial genomes! It's the successor to Trycycler, designed to be faster and less reliant on user intervention.
submitted by: Istvan Albert
pipemake: A pipeline creation tool using Snakemake for reproducible analysis of biological datasets | bioRxiv (www.biorxiv.org)
pipemake: A pipeline creation tool using Snakemake for reproducible analysis of biological datasets
It reminds me of a joke:
- A bioinformatician once had a problem: Snakemake was too complicated.
- So they decided to write Pipemake, an easy-to-use software tool to generate Snakemake files.
- Now they had two problems.
I hope I am wrong, though - still worth a chuckle.
Link to repo: https://github.com/kocherlab/pipemake
submitted by: Istvan Albert
GeneSetCluster 2.0: a comprehensive toolset for summarizing and integrating gene-sets analysis (www.biorxiv.org)
We introduce GeneSetCluster 2.0 which substantially improves upon its predecessor. This update presents a new methodology for addressing duplicated gene-sets and incorporates a seriation-based clustering algorithm that reorders data, enabling the identification of patterns.
submitted by: Istvan Albert
Simply Statistics: Biologists, stop putting UMAP plots in your papers (simplystatistics.org)
Biologists, stop putting UMAP plots in your papers
submitted by: Istvan Albert
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