Herald:The Biostar Herald for Thursday, April 28, 2022
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This edition of the Herald was brought to you by contribution from zx8754, Istvan Albert, Yannick Wurm, and was edited by Istvan Albert,

Improved sequence mapping using a complete reference genome and lift-over | bioRxiv (www.biorxiv.org)

Complete, telomere-to-telomere genome assemblies promise improved analyses and the discovery of new variants, but many essential genomic resources remain associated with older reference genomes. Thus, there is a need to translate genomic features and read alignments between references. Here we describe a new method called levioSAM2 that accounts for reference changes and performs fast and accurate lift-over between assemblies using a whole-genome map. In addition to enabling the use of multiple references, we demonstrate that aligning reads to a high-quality reference (e.g. T2T-CHM13) and lifting to an older reference (e.g. GRCh38) actually improves the accuracy of the resulting variant calls on the old reference.

submitted by: Istvan Albert

SequenceServer: Powerful software for running BLAST and visualizing results | SequenceServer (sequenceserver.com)

SequenceServer 2.0 has been released.

submitted by: Yannick Wurm

GLIMPSE (odelaneau.github.io)

GLIMPSE is a phasing and imputation method for large-scale low-coverage sequencing studies.

submitted by: zx8754

Using prototyping to choose a bioinformatics workflow management system (journals.plos.org)

To select a workflow management system, a rapid survey of available systems was undertaken, and candidates were shortlisted: Snakemake, cwltool, Toil, and Nextflow

submitted by: Istvan Albert

submitted by: Istvan Albert

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