Herald:The Biostar Herald for Wednesday, October 13, 2021
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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,


submitted by: Istvan Albert


submitted by: Istvan Albert


Confronting false discoveries in single-cell differential expression | Nature Communications (www.nature.com)

Here, we show that the relative performance of these methods is contingent on their ability to account for variation between biological replicates. Methods that ignore this inevitable variation are biased and prone to false discoveries. Indeed, the most widely used methods can discover hundreds of differentially expressed genes in the absence of biological differences. To exemplify these principles, we exposed true and false discoveries of differentially expressed genes in the injured mouse spinal cord.

submitted by: Istvan Albert


https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btab705/6384570

Now minimap2 v2.22 can more accurately map long reads to highly repetitive regions and align through insertions or deletions up to 100kb by default, addressing major weakness in minimap2 v2.18 or earlier.

submitted by: Istvan Albert


GitHub - brentp/slivar: variant expressions, annotation, and filtering for great good. (github.com)

slivar: filter/annotate variants in VCF/BCF format with simple expressions

slivar is a set of command-line tools that enables rapid querying and filtering of VCF files. It facilitates operations on trios and groups and allows arbitrary expressions using simple javascript.

submitted by: Istvan Albert


GitHub - HKU-BAL/Clair: Clair: Exploring the limit of using deep neural network on pileup data for germline variant calling (github.com)

In this study, we present Clair, the successor to Clairvoyante, a program for fast and accurate germline small variant calling, using single molecule sequencing data. For ONT data, Clair achieves the best precision, recall and speed as compared to several competing programs, including Clairvoyante, Longshot and Medaka.

submitted by: Istvan Albert


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