Herald:The Biostar Herald for Monday, January 17, 2022
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Biostar 730

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,


Inverting the model of genomics data sharing with the NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-space: Cell Genomics00106-3) (www.cell.com)

By inverting the traditional model of data sharing, the AnVIL eliminates the need for data movement while also adding security measures for active threat detection and monitoring and provides scalable, shared computing resources for any researcher. We describe the core data management and analysis components of the AnVIL, which currently consists of Terra, Gen3, Galaxy, RStudio/Bioconductor, Dockstore, and Jupyter, and describe several flagship genomics datasets available within the AnVIL.

submitted by: Istvan Albert


https://academic.oup.com/bioinformatics/article/32/17/2686/2450738

That is, relative to other fields, bioinformatics produces some programs that are extremely widely adopted and cited, yet there are fewer of intermediate success.

submitted by: Istvan Albert


Partitioning RNAs by length improves transcriptome reconstruction from short-read RNA-seq data | Nature Biotechnology (www.nature.com)

. Here we introduce Ladder-seq, an approach that separates transcripts according to their lengths before sequencing and uses the additional information to improve the quantification and assembly of transcripts.

submitted by: Istvan Albert


An investigation of irreproducibility in maximum likelihood phylogenetic inference | Nature Communications (www.nature.com)

In this study, we found that ~9 to ~18% of single-gene phylogenies in 15 phylogenomic data sets were topologically irreproducible when analyzed by two widely used ML programs on a supercomputing cluster (Figs. 1 and 2). In addition to sequence alignment, program, substitution model, number of tree searches, and random starting seed number, which are known contributors, we further found that low phylogenetic informativeness, processor type, and multithreading contribute to the observed irreproducibility, with the effects of multithreading being program-specific

submitted by: Istvan Albert


Cool command line replacements

submitted by: Istvan Albert


Release Release 1.5.0 · fulcrumgenomics/fgbio · GitHub (github.com)

A bunch of tools that look and feel just like Picard

submitted by: Istvan Albert


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