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,
Genome assembly in the telomere-to-telomere era | Nature Reviews Genetics (www.nature.com)
Here, we review recent progress on assembly algorithms and protocols, with a focus on how to derive near-telomere-to-telomere assemblies. We also discuss the additional developments that will be required to resolve remaining assembly gaps and to assemble non-diploid genomes.
submitted by: Istvan Albert
Measuring, visualizing, and diagnosing reference bias with biastools | Genome Biology | Full Text (genomebiology.biomedcentral.com)
Many bioinformatics methods seek to reduce reference bias, but no methods exist to comprehensively measure it. Biastools analyzes and categorizes instances of reference bias. It works in various scenarios: when the donor’s variants are known and reads are simulated; when donor variants are known and reads are real; and when variants are unknown and reads are real. Using biastools, we observe that more inclusive graph genomes result in fewer biased sites. We find that end-to-end alignment reduces bias at indels relative to local aligners.
submitted by: Istvan Albert
ScienceDirect (www.sciencedirect.com)
This comprehensive review delves into the intricate interplay between cutting-edge long read sequencing technologies, assembly methodologies, and the ever-evolving field of genomics. With a focus on addressing the pivotal challenges and harnessing the opportunities presented by these advancements, we provide an in-depth exploration of the crucial factors influencing the selection of optimal strategies for achieving robust and insightful genome assemblies.
submitted by: Istvan Albert
Release 1.20 of HTSlib, SAMtools, and BCFtools is now available from GitHub. See https://t.co/oBT6uOcTtz for links to tarballs and release notes.
— Samtools Team (@htslib) April 15, 2024
Release 1.20 of HTSlib, SAMtools, and BCFtools is now available from GitHub. See https://t.co/oBT6uOcTtz for links to tarballs and release notes.
— Samtools Team (@htslib) April 15, 2024Release notes:
- samtools: https://github.com/samtools/samtools/releases/tag/1.20
- bcftools: https://github.com/samtools/bcftools/releases/tag/1.20
- htslib: https://github.com/samtools/htslib/releases/tag/1.20
submitted by: Istvan Albert
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bwa 0.7.18 released !
https://github.com/lh3/bwa/releases/tag/v0.7.18