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,
Improved sequence mapping using a complete reference genome and lift-over | bioRxiv (www.biorxiv.org)
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
The MUMmer Home Page (mummer.sourceforge.net)
MUMmer is a system for rapidly aligning DNA and protein sequences
MUMmer is perhaps among the greatest bioinformatics computer programs ever written. Originally published in 1999, it has seen new versions released in 2002, 2004 then 2018
The greatness of MUMer is best demonstrated not just by the number of its citations, but by the way that it has become a foundation for countless other approaches.
A simple shell script that uses awk to parse and filter MUMmer output can still be published as a standalone Bioinformatics protocol in one of the most selective bioinformatics journals... If that is not the ultimate homage to MUMmer, not sure what is...
MUM&Co: accurate detection of all SV types through whole-genome alignment
submitted by: Istvan Albert
Annotation of structural variants with reported allele frequencies and related metrics from multiple datasets using SVAFotate | bioRxiv (www.biorxiv.org)
We introduce SVAFotate, a software tool for SV matching that enables the annotation of SVs with variant allele frequency and related information. These annotations are derived from known SV datasets which are incorporated by SVAFotate. As a result, VCF files annotated by SVAFotate offer a variety of annotations to aid in the stratification of SVs as common or rare in the broader human population.
submitted by: Istvan Albert
GitHub - RealTimeGenomics/rtg-tools: RTG Tools: Utilities for accurate VCF comparison and manipulation (github.com)
RTG Tools is a subset of RTG Core that includes several useful utilities for dealing with VCF files and sequence data. Probably the most interesting is the vcfeval command which performs sophisticated comparison of VCF files.
submitted by: Istvan Albert
GitHub - genome-in-a-bottle/giab_data_indexes: This repository contains data indexes from NIST's Genome in a Bottle project. (github.com)
This repository contains data indexes from NIST's Genome in a Bottle (GIAB) project.
submitted by: Istvan Albert
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