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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
Currently in the hellscape of which pipeline/workflow manager to use for some methods, with clinical use as a consideration.
Any advice?
Also poll of options I'm tossing up
— James Ferguson (@Psy_Fer_) April 19, 2022
Currently in the hellscape of which pipeline/workflow manager to use for some methods, with clinical use as a consideration.
Any advice?
Also poll of options I'm tossing up
submitted by: Istvan Albert
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