Herald:The Biostar Herald for Monday, May 01, 2023
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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

GitHub - bluenote-1577/skani: Fast, robust ANI and aligned fraction for metagenomic genomes and contigs (github.com)

skani is a program for calculating average nucleotide identity (ANI) from DNA sequences (contigs/MAGs/genomes) for ANI > ~80%.

submitted by: Istvan Albert

GitHub - owkin/PyDESeq2: A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA. (github.com)

This package is a python implementation of the DESeq2 method for differential expression analysis (DEA) with bulk RNA-seq data, originally in R. It aims to facilitate DEA experiments for python users.

submitted by: Istvan Albert

submitted by: Istvan Albert

vcfdist: Accurately benchmarking phased small variant calls in human genomes | bioRxiv (www.biorxiv.org)

Accurately benchmarking small variant calling accuracy is critical for the continued improvement of human whole genome sequencing. In this work, we show that current variant calling evaluations are biased towards certain variant representations and may misrepresent the relative performance of different variant calling pipelines.

submitted by: Istvan Albert

GitHub - brwnj/covviz: Multi-sample genome coverage viewer to observe large, coverage-based anomalies alongside annotations and sample metadata (github.com)

Coverage visualization; a many-sample coverage browser.

The aim of covviz is to highlight regions of significant (passing the user's z-score threshold) and sustained (beyond user specified distance) deviation of coverage depth from the majority of samples. Significance is determined using z-scores for all samples at all points using median absolute deviation. In order for regions to be highlighted, points must be significant consecutively throughout a user specified distance.

submitted by: Istvan Albert

JBrowse 2: a modular genome browser with views of synteny and structural variation | Genome Biology | Full Text (genomebiology.biomedcentral.com)

We present JBrowse 2, a general-purpose genome annotation browser offering enhanced visualization of complex structural variation and evolutionary relationships. It retains core features of JBrowse while adding new views for synteny, dotplots, breakpoints, gene fusions, and whole-genome overviews. It allows users to share sessions, open multiple genomes, and navigate between views. It can be embedded in a web page, used as a standalone application, or run from Jupyter notebooks or R sessions. These improvements are enabled by a ground-up redesign using modern web technology. We describe application functionality, use cases, performance benchmarks, and implementation notes for web administrators and developers.

submitted by: Istvan Albert

YACHT: an ANI-based statistical test to detect microbial presence/absence in a metagenomic sample | bioRxiv (www.biorxiv.org)

In metagenomics, the study of environmentally associated microbial communities from their sampled DNA, one of the most fundamental computational tasks is that of determining which genomes from a reference database are present or absent in a given sample metagenome. While tools exist to answer this question, all existing approaches to date return point estimates, with no associated confidence or uncertainty associated with it. [...] In this work, we present solutions for these issues by introducing the algorithm YACHT: Yes/No Answers to Community membership via Hypothesis Testing.

submitted by: Istvan Albert

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thanks for highlighting jbrowse 2!


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