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,
Centrifuger: lossless compression of microbial genomes for efficient and accurate metagenomic sequence classification | Genome Biology | Full Text (genomebiology.biomedcentral.com)
Centrifuger is an efficient taxonomic classification method that compares sequencing reads against a microbial genome database [...] Furthermore, the lossless compression and the unconstrained match length help Centrifuger achieve greater accuracy than competing methods at lower taxonomic levels.
submitted by: Istvan Albert
Exploring the Genetic Basis of Variation in Gene Predictions with a Synthetic Association Study | PLOS ONE (journals.plos.org)
Here we introduce an alternative strategy: a “synthetic association study” in which we computationally predict molecular phenotypes on artificial genomes containing randomly sampled combinations of polymorphic alleles, and perform a classical association study to identify genotypes underlying variation in these computationally predicted annotations.
submitted by: Istvan Albert
https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btae275/7658303
In this paper, we introduce the Bioinformatics Tool Recommendation system (BTR), a deep learning model designed to recommend suitable tools for a given workflow-in-progress. BTR leverages recent advances in graph neural network technology, representing the workflow as a graph to capture essential context. Natural language processing techniques enhance tool recommendations by analyzing associated tool descriptions.
submitted by: Istvan Albert
Analysis and benchmarking of small and large genomic variants across tandem repeats | Nature Biotechnology (www.nature.com)
We curated variants from the Genome in a Bottle (GIAB) HG002 individual to create a TR dataset to benchmark existing and future TR analysis methods. We also present an improved variant comparison method that handles variants greater than 4 bp in length and varying allelic representation. The 8.1% of the genome covered by the TR catalog holds ~24.9% of variants per individual, including 124,728 small and 17,988 large variants for the GIAB HG002 ‘truth-set’ TR benchmark. We demonstrate the utility of this pipeline across short-read and long-read technologies.
submitted by: Istvan Albert
https://github.com/rust-bio/rust-bio
This library provides Rust implementations of algorithms and data structures useful for bioinformatics. All provided implementations are rigorously tested via continuous integration.
submitted by: Istvan Albert
NextDenovo: an efficient error correction and accurate assembly tool for noisy long reads | Genome Biology | Full Text (genomebiology.biomedcentral.com)
Here, we present NextDenovo, an efficient error correction and assembly tool for noisy long reads, which achieves a high level of accuracy in genome assembly. We apply NextDenovo to assemble 35 diverse human genomes from around the world using Nanopore long-read data.
submitted by: Istvan Albert
GitHub - Kuanhao-Chao/LiftOn: 🚀 LiftOn: Accurate annotation mapping for GFF/GTF across assemblies (github.com)
LiftOn is a homology-based lift-over tool using both DNA-DNA alignments (from Liftoff, credits to Dr. Alaina Shumate) and protein-DNA alignments (from miniprot, credits to Dr. Heng Li) to accurately map annotations between genome assemblies of the same or different species.
submitted by: Istvan Albert
📢📢Dear friends, I'm thrilled to introduce LiftOn, our new homology-based annotation lift-over tool🚀 Join my talk at @RECOMBseq Saturday April 27th at 2:50PM!@JakobHeinz9 @celinehohzm @alan_mayonnaise @alaina_shumate @elapertea @StevenSalzberg1
🔗https://t.co/1IQjtk5LkD (1/5)
— Kuan-Hao Chao (@KuanHaoChao) April 25, 2024
📢📢Dear friends, I'm thrilled to introduce LiftOn, our new homology-based annotation lift-over tool🚀 Join my talk at @RECOMBseq Saturday April 27th at 2:50PM!@JakobHeinz9 @celinehohzm @alan_mayonnaise @alaina_shumate @elapertea @StevenSalzberg1
🔗https://t.co/1IQjtk5LkD (1/5)
submitted by: Istvan Albert
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