Herald:The Biostar Herald for Wednesday, September 06, 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,

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Check our new paper “Predicting RNA-seq coverage from DNA sequence as a unifying model of gene regulation”. https://t.co/W7GYZgGbgh

— David Kelley (@drklly) September 2, 2023

submitted by: Istvan Albert

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I've been coding in Python for 8 years now. ⏳

If I were to start over again in 2023, here's a roadmap:👇 pic.twitter.com/PszcgafCUd

— Akshay 🚀 (@akshay_pachaar) August 31, 2023

submitted by: Istvan Albert

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Sandy | Sandy is a bioinformatics tool that provides a simple and extensible engine to simulate single-end and paired-end reads for whole-genome and RNA sequencing. (galantelab.github.io)

Sandy is a bioinformatics tool that provides a simple engine to simulate next-generation sequencing (NGS) reads for genomic and transcriptomic pipelines. Simulated data works as experimental control - a key step to optimize NGS analysis - in comparison to hypothetical models. Sandy is a straightforward, easy-to-use, fast and highly customizable tool that generates reads requiring only a fasta file as input.

submitted by: Istvan Albert

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Terrifying plot for those working in microbiome profiling pic.twitter.com/8vKXX3uacW

— Mick W@tson ↙️ (@BioMickWatson) August 29, 2023

submitted by: Istvan Albert

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Metagenomic profiling pipelines improve taxonomic classification for 16S amplicon sequencing data | Scientific Reports (www.nature.com)

We evaluated the tools DADA2, QIIME 2, Mothur, PathoScope 2, and Kraken 2 in conjunction with reference libraries from Greengenes, SILVA, Kraken 2, and RefSeq.[...] These findings support PathoScope and Kraken 2 as fully capable, competitive options for genus- and species-level 16S amplicon sequencing data analysis, whole genome sequencing, and metagenomics data tools.

submitted by: Istvan Albert

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somalier can find relatedness among thousands (or a handful if that's what you have) of samples in seconds. latest release updates a lesser-used feature to find your own sites with which to calculate kinship: https://t.co/etNxULXsk4

thanks @johanneskoester for reporting!

— brent pedersen (@brent_p) August 28, 2023

submitted by: Istvan Albert

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https://academic.oup.com/bioinformaticsadvances/advance-article/doi/10.1093/bioadv/vbad107/7252269

We introduce VCFshiny, an R package that features a user-friendly web interface enabling interactive annotation, interpretation, and visualization of variant information stored in VCF files. VCFshiny offers two annotation methods, Annovar and VariantAnnotation, to add annotations such as genes or functional impact. Annotated VCF files are deemed acceptable inputs for the purpose of summarizing and visualizing variant information.

submitted by: Istvan Albert

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