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 zx8754, Istvan Albert, and was edited by Istvan Albert,
Benchmarking of variant calling software for whole-exome sequencing using gold standard datasets | Scientific Reports (www.nature.com)
This study benchmarks four non-programming variant calling software namely, Illumina BaseSpace Sequence Hub (Illumina), CLC Genomics Workbench (CLC), Partek Flow, and Varsome Clinical, for the variant calling of three Genome in a Bottle (GIAB) whole-exome sequencing datasets (HG001, HG002 and HG003).
submitted by: Istvan Albert
Which programming language should I use? A guide for early-career researchers (www.nature.com)
Which programming language should I use? A guide for early-career researchers Computer scientists and bioinformaticians address four key questions to help rookie coders to make the right choice. By Jeffrey M. Perkel
submitted by: zx8754
Short RNA-seq read alignment with minimap2 (lh3.github.io)
TL;DR: the new preset splice:sr in minimap2 can align short RNA-seq reads. It is similar to STAR in resource usage, approaches STAR in junction accuracy, and is overall better at SNP calling.
submitted by: Istvan Albert
The phased pan-genome of tetraploid European potato | Nature (www.nature.com)
Here we present the pan-genome of European potatoes generated from phased genome assemblies of ten historical potato cultivars, which includes approximately 85% of all haplotypes segregating in Europe. Sequence diversity between the haplotypes was extremely high (for example, 20× higher than in humans), owing to numerous introgressions from wild potato species.
submitted by: Istvan Albert
GitHub - cidgoh/bacpaq: Bacterial Genomics workflow for short(Illumina) and long-read (Oxford Nanopore) sequencing data (github.com)
bacpaq is a bioinformatics best-practice pipeline for bacterial genomic analysis for short-reads (Illumina) and long-reads (Oxford Nanopore) sequencing data.
submitted by: Istvan Albert
Guidelines for releasing a variant effect predictor | Genome Biology | Full Text (genomebiology.biomedcentral.com)
Computational methods for assessing the likely impacts of mutations, known as variant effect predictors (VEPs), are widely used in the assessment and interpretation of human genetic variation, as well as in other applications like protein engineering. Many different VEPs have been released, and there is tremendous variability in their underlying algorithms, outputs, and the ways in which the methodologies and predictions are shared. This leads to considerable difficulties for users trying to navigate the selection and application of VEPs. Here, to address these issues, we provide guidelines and recommendations for the release of novel VEPs.
submitted by: Istvan Albert
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