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,
GitHub - bokulich-lab/RESCRIPt: REference Sequence annotation and CuRatIon Pipeline (github.com)
REference Sequence annotation and CuRatIon Pipeline
RESCRIPt is a python 3 package to support a variety of operations for managing and curating reference sequence databases, DNA/RNA sequence data, and taxonomic data.
submitted by: Istvan Albert
https://academic.oup.com/bioinformatics/article/35/3/421/5055585
General-purpose processors can now contain many dozens of processor cores and support hundreds of simultaneous threads of execution. To make best use of these threads, genomics software must contend with new and subtle computer architecture issues. We discuss some of these and propose methods for improving thread scaling in tools that analyze each read independently, such as read aligners.
submitted by: Istvan Albert
Sustained software development, not number of citations or journal choice, is indicative of accurate bioinformatic software | Genome Biology | Full Text (genomebiology.biomedcentral.com)
We find that software speed, author reputation, journal impact, number of citations and age are unreliable predictors of software accuracy. This is unfortunate because these are frequently cited reasons for selecting software tools.
submitted by: Istvan Albert
If you work w/ single-cell RNA-seq & are performing RNA velocity analyses, you might find this @GorinGennady et al. preprint w/ Meichen Fang & Tara Chari of interest. It's a deep dive into the method, and navigation of the 67 pages may be aided w/ this🧵1/https://t.co/6ESXDbt1MC
— Lior Pachter (@lpachter) February 14, 2022
If you work w/ single-cell RNA-seq & are performing RNA velocity analyses, you might find this @GorinGennady et al. preprint w/ Meichen Fang & Tara Chari of interest. It's a deep dive into the method, and navigation of the 67 pages may be aided w/ this🧵1/https://t.co/6ESXDbt1MC
— Lior Pachter (@lpachter) February 14, 2022submitted by: Istvan Albert
GitHub - pachterlab/GFCP_2022: RNA velocity validation (github.com)
This directory contains scripts and code to generate all the figures in the manuscript "RNA velocity unraveled" by Gennady Gorin, Meichen Fang, Tara Chari, and Lior Pachter.
submitted by: Istvan Albert
Comparison of GATK and DeepVariant by trio sequencing | Scientific Reports (www.nature.com)
While next-generation sequencing (NGS) has transformed genetic testing, it generates large quantities of noisy data that require a significant amount of bioinformatics to generate useful interpretation. The accuracy of variant calling is therefore critical. Although GATK HaplotypeCaller is a widely used tool for this purpose, newer methods such as DeepVariant have shown higher accuracy in assessments of gold-standard samples for whole-genome sequencing (WGS) and whole-exome sequencing (WES), but a side-by-side comparison on clinical samples has not been performed.
submitted by: Istvan Albert
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