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,
Human microbiome myths and misconceptions | Nature Microbiology (www.nature.com)
We hope that, by illustrating just a few examples of microbiome myths and misconceptions, we can draw increased attention to the potential problems of over-simplification and insufficient critical assessment in the microbiome literature.
submitted by: Istvan Albert
Identification of errors in draft genome assemblies at single-nucleotide resolution for quality assessment and improvement | Nature Communications (www.nature.com)
Here, we develop a new reference-free tool, Clipping information for Revealing Assembly Quality (CRAQ), which maps raw reads back to assembled sequences to identify regional and structural assembly errors based on effective clipped alignment information. Error counts are transformed into corresponding assembly evaluation indexes to reflect the assembly quality at single-nucleotide resolution.
Editor note: CRAQ ... why is this acronym so familiar, ah yes, the decade old yet still timeless Biostar post:
"Crac: Funny And/Or Weird Names For Bioinformatics Tools"
Crac: Funny And/Or Weird Names For Bioinformatics Tools
submitted by: Istvan Albert
NCBI Datasets: Easily Access and Download Sequence Data and Metadata - NCBI Insights (ncbiinsights.ncbi.nlm.nih.gov)
Effective May 2024, NCBI Datasets will replace legacy Genome and Assembly web resources
submitted by: Istvan Albert
Quick Start — phykit documentation (jlsteenwyk.com)
PhyKIT, a toolkit for the UNIX shell environment with numerous functions that process multiple sequence alignments and phylogenies for broad applications
submitted by: Istvan Albert
https://academic.oup.com/bioinformatics/article/37/16/2325/6131675
We introduce PhyKIT, a toolkit for the UNIX shell environment with 30 functions that process MSAs and trees, including but not limited to estimation of mutation rate, evaluation of sequence composition biases, calculation of the degree of violation of a molecular clock and collapsing bipartitions (internal branches) with low support
submitted by: Istvan Albert
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