Herald:The Biostar Herald for Tuesday, September 26, 2023
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10 months ago
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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, Shred, and was edited by Istvan Albert,

GIA: A genome interval arithmetic toolkit for high performance interval set operations | bioRxiv (www.biorxiv.org)

The study introduces GIA (Genomic Interval Arithmetic) and BEDRS, a novel command-line tool and a rust library that significantly enhance the performance of genomic interval analysis. GIA outperforms existing tools like BEDOPS, BEDTools, and GenomicRanges by a factor of 2x to 20x across a range of operations.

submitted by: Istvan Albert

GitHub - glarue/jgi-query: A simple command-line tool to download data from Joint Genome Institute databases (github.com)

A command-line tool for querying and downloading from databases hosted by the Joint Genome Institute (JGI). Useful for accessing JGI data from command-line-only resources such as remote servers, or as a lightweight alternative to JGI's other GUI-based download tools.

submitted by: Istvan Albert

Evaluation of taxonomic classification and profiling methods for long-read shotgun metagenomic sequencing datasets | BMC Bioinformatics (link.springer.com)

Here, we perform a critical benchmarking study using 11 methods, including five methods designed specifically for long reads. We applied these tools to several mock community datasets generated using Pacific Biosciences (PacBio) HiFi or Oxford Nanopore Technology sequencing, and evaluated their performance based on read utilization, detection metrics, and relative abundance estimates.

submitted by: Istvan Albert

Accurate proteome-wide missense variant effect prediction with AlphaMissense (www.science.org)

Alphamissense is the new model developed by Deepmind to predict the effect of missense variants on proteins. Already available as a VEP plugin.

submitted by: Shred

Rarefaction is currently the best approach to control for uneven sequencing effort in amplicon sequence analyses | bioRxiv (www.biorxiv.org)

I generated community distributions based on 12 published datasets where I was able to assess the ability of multiple methods to control for uneven sequencing effort. Rarefaction was the only method that could control for variation in uneven sequencing effort when measuring commonly used alpha and beta diversity metrics.

submitted by: Istvan Albert

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