Herald:The Biostar Herald for Monday, January 30, 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,


Structural variation across 138,134 samples in the TOPMed consortium | bioRxiv (www.biorxiv.org)

Here we present a catalog of 355,667 SVs (59.34% novel) across autosomes and the X chromosome (50bp+) from 138,134 individuals in the diverse TOPMed consortium. We describe our methodologies for SV inference resulting in high variant quality and >90% allele concordance compared to long-read de-novo assemblies of well-characterized control samples. We demonstrate utility through significant associations between SVs and important various cardio-metabolic and hemotologic traits.

submitted by: Istvan Albert


A publishing infrastructure for AI-assisted academic authoring (greenelab.github.io)

In this work we investigate how models with advanced natural language processing capabilities can be used to reduce the time-consuming process of writing and revising scholarly manuscripts. [...] Our results suggest that these models can capture the concepts in the scholarly text and produce high-quality revisions that improve clarity. Given the amount of time that researchers put into crafting prose, we anticipate that this advance will revolutionize the type of knowledge work performed by academics.

submitted by: Istvan Albert


ggCaller 1.3.0 documentation (ggcaller.readthedocs.io)

ggCaller is a novel bacterial gene annotation and pangenome analysis tool, designed to enable fast, accurate analysis of large single-species genome datasets.

submitted by: Istvan Albert


Accurate and fast graph-based pangenome annotation and clustering with ggCaller | bioRxiv (www.biorxiv.org)

Here, we introduce the open-source software graph-gene-caller ggCaller the combines gene prediction, functional annotation and clustering into a single step using population-wide de Bruijn Graphs, removing redundancy in gene annotation, and resulting in more accurate gene predictions and orthologue clustering.

submitted by: Istvan Albert


GitHub - TileDB-Inc/TileDB-VCF: Efficient variant-call data storage and retrieval library using the TileDB storage library. (github.com)

A C++ library for efficient storage and retrieval of genomic variant-call data using TileDB Embedded.

submitted by: Istvan Albert


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