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, natay,
https://www.sciencedaily.com/releases/2020/07/200702113649.htm
The principle of "dog years" states that every year in a dog's life is equivalent to 7 years of human life.
Well, Bioinformatics has its "dog years" as well - basically, that high-impact, cool, bioinformatics review article from 2016 describes methodologies that practically 5 * 7 = 35 years old.
Fear not though, bioinformaticians have also come up with a more accurate formula for dog years, where instead of multiplying by 7 the correction formula is:
real age = 16 * log(age) + 31
Which makes that high-impact, cool, bioinformatics review article from 2016 more than 55 years old. Do you really want to use a 55-year-old technology? ... hmmm
submitted by: Istvan Albert
A quick start guide to a portable and simplified alevin-fry pipeline (combine-lab.github.io)
Here, we show how to perform a completely analysis on the 1k PBMCs from a Healthy Donor data from 10X Genomics. This run through includes all steps, even extracting the splici sequence and building the salmon index, which you typically would not do per-sample. To make this sample as easy as possible to follow, we have bundled all of the required software and utilities in a singularity container that we use in the commands below.
submitted by: Istvan Albert
Is it time to change the reference genome? | Genome Biology | Full Text (genomebiology.biomedcentral.com)
The use of the human reference genome has shaped methods and data across modern genomics. This has offered many benefits while creating a few constraints. In the following opinion, we outline the history, properties, and pitfalls of the current human reference genome. In a few illustrative analyses, we focus on its use for variant-calling, highlighting its nearness to a ‘type specimen’. We suggest that switching to a consensus reference would offer important advantages over the continued use of the current reference with few disadvantages.
submitted by: Istvan Albert
De Novo Assembly of Two Swedish Genomes Reveals Missing Segments from the Human GRCh38 Reference and Improves Variant Calling of Population-Scale Sequencing Data (www.ncbi.nlm.nih.gov)
The current human reference sequence (GRCh38) is a foundation for large-scale sequencing projects. However, recent studies have suggested that GRCh38 may be incomplete and give a suboptimal representation of specific population groups. Here, we performed a de novo assembly of two Swedish genomes that revealed over 10 Mb of sequences absent from the human GRCh38 reference in each individual.
submitted by: Istvan Albert
A complete reference genome improves analysis of human genetic variation | bioRxiv (www.biorxiv.org)
Compared to its predecessors, the Telomere-to-Telomere CHM13 genome adds nearly 200 Mbp of sequence, corrects thousands of structural errors, and unlocks the most complex regions of the human genome to clinical and functional study. Here we demonstrate how the new reference universally improves read mapping and variant calling for 3,202 and 17 globally diverse samples sequenced with short and long reads, respectively.
submitted by: Istvan Albert
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