Herald:The Biostar Herald for Tuesday, December 27, 2022
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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,

BioNumPy documentation — bionumpy documentation (bionumpy.github.io)

There is some buzz about bionumpy, though after reading the docs I don't quite understand its main use-cases.

submitted by: Istvan Albert

GitHub - igvteam/igv.js: Embeddable genomic visualization component based on the Integrative Genomics Viewer (github.com)

igv.js is an embeddable interactive genome visualization component developed by the Integrative Genomics Viewer (IGV) team.

submitted by: Istvan Albert


igv.js is an embeddable JavaScript implementation of the Integrative Genomics Viewer (IGV). It can be easily dropped into any web page with a single line of code and has no external dependencies. The viewer runs completely in the web browser, with no backend server and no data pre-processing required.

submitted by: Istvan Albert

submitted by: Istvan Albert

Comparison of calling pipelines for whole genome sequencing: an empirical study demonstrating the importance of mapping and alignment | Scientific Reports (www.nature.com)

The aim of this study was the comparison of 6 WGS data pre-processing pipelines, involving two mapping and alignment approaches (GATK utilizing BWA-MEM2 2.2.1, and DRAGEN 3.8.4) and three variant calling pipelines (GATK, DRAGEN 3.8.4 and DeepVariant 1.1.0).

submitted by: Istvan Albert

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The tweet referencing dynamical models of RNA transcription (https://www.nature.com/articles/s41467-022-34857-7) has a successor article in PLOS specifically on RNA velocity by (many) of the same authors: https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1010492


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