Herald:The Biostar Herald for Wednesday, February 15, 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,


Stop the peer-review treadmill. I want to get off (www.nature.com)

Faced with a deluge of papers, journal editors are struggling to find willing peer reviewers.

[...] estimated that researchers globally, in aggregate, spent the equivalent of more than 15,000 years on peer review in 2020 alone

submitted by: Istvan Albert


GitHub - tjiangHIT/cuteSV: Long read based human genomic structural variation detection with cuteSV (github.com)

We propose cuteSV, a sensitive, fast and scalable long-read-based SV detection approach. cuteSV uses tailored methods to collect the signatures of various types of SVs and employs a clustering-and-refinement method to analyze the signatures to implement sensitive SV detection. Benchmarks on real Pacific Biosciences (PacBio) and Oxford Nanopore Technology (ONT) datasets demonstrate that cuteSV has better yields and scalability than state-of-the-art tools.

submitted by: Istvan Albert


https://academic.oup.com/bioinformatics/article/39/1/btad048/6998200

The annotations generated as a result of these experiments are generally biased towards a small subset of less informative Gene Ontology (GO) terms. Identifying and removing biases from protein function annotation databases is important since biases impact our understanding of protein function by providing a poor picture of the annotation landscape.

We introduce GOThresher, a Python tool that identifies and removes biases in function annotations from protein function annotation databases.

submitted by: Istvan Albert


submitted by: Istvan Albert


https://academic.oup.com/nar/article/51/1/e3/6775383

Here, we introduce echtvar, which efficiently encodes population variants and annotation fields into a compressed archive that can be used for rapid variant annotation and filtering. [...] We show that echtvar is faster and uses less space than existing tools and that it can effectively reduce the number of candidate variants.

submitted by: Istvan Albert


GitHub - torognes/vsearch: Versatile open-source tool for microbiome analysis (github.com)

We have implemented a tool called VSEARCH which supports de novo and reference based chimera detection, clustering, full-length and prefix dereplication, rereplication, reverse complementation, masking, all-vs-all pairwise global alignment, exact and global alignment searching, shuffling, subsampling and sorting. It also supports FASTQ file analysis, filtering, conversion and merging of paired-end reads.

submitted by: Istvan Albert


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