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 zx8754, GenoMax, Istvan Albert, and was edited by GenoMax, Istvan Albert,
Impact of genome build on RNA-seq interpretation and diagnostics (doi.org)
Paper studied the effect of the hg19, hg38, and CHM13 genome builds on expression quantification and outlier detection in 386 rare disease and familial control samples
submitted by: GenoMax
A 160 Gbp fork fern genome shatters size record for eukaryotes (doi.org)
Genome size champion. A fork fern. 160 billion bp.
submitted by: GenoMax
Benchmarking of bioinformatics tools for the hybrid de novo assembly of human whole-genome sequencing data | bioRxiv (www.biorxiv.org)
Accurate and complete de novo assembled genomes sustain variant identification and catalyze the discovery of new genomic features and biological functions. However, accurate and precise de novo assemblies of large and complex genomes remains a challenging task. [...] Here we benchmarked 11 different pipelines including four long-read only assemblers and three hybrid assemblers, combined with four polishing schemes for de novo genome assembly of a human reference material sequenced with Oxford Nanopore Technologies and Illumina.
submitted by: Istvan Albert
Accurate, scalable, and fully automated inference of species trees from raw genome assemblies using ROADIES | bioRxiv (www.biorxiv.org)
In this paper, we present ROADIES, a novel pipeline for species tree inference from raw genome assemblies that is fully automated, easy to use, scalable, free from reference bias, and provides flexibility to adjust the tradeoff between accuracy and runtime. The ROADIES pipeline eliminates the need to align whole genomes, choose a single reference species, or pre-select loci such as functional genes found using cumbersome annotation steps. Moreover, it leverages recent advances in phylogenetic inference to allow multi-copy genes, eliminating the need to detect orthology. Using the genomic datasets released from large-scale sequencing consortia across three diverse life forms (placental mammals, pomace flies, and birds), we show that ROADIES infers species trees that are comparable in quality with the state-of-the-art approaches but in a fraction of the time.
submitted by: Istvan Albert
x.com (x.com)
The GRanges Rust library and command line tool
GRanges is a Rust library for working with genomic ranges and their associated data. It aims to make it easy to write extremely performant genomics tools that work with genomic range data (e.g. BED, GTF/GFF, VCF, etc). Internally, GRanges uses the very fast coitrees interval tree library written by Daniel C. Jones for overlap operations. In preliminary benchmarks, GRanges tools can be 10%-30% faster than similar functionality in bedtools2.
https://www.biorxiv.org/content/10.1101/2024.05.24.595786v1 https://github.com/vsbuffalo/granges
submitted by: zx8754
Comprehensive analysis of microbial content in whole-genome sequencing samples from The Cancer Genome Atlas project | bioRxiv (www.biorxiv.org)
In recent years, a growing number of publications have reported the presence of microbial species in human tumors and of mixtures of microbes that appear to be highly specific to different cancer types. Our recent re-analysis of data from three cancer types revealed that technical errors have caused erroneous reports of numerous microbial species reportedly found in sequencing data from The Cancer Genome Atlas (TCGA) project. [...]Our results expand upon and reinforce our recent findings, which showed that the presence of microbes is far smaller than had been previously reported, and that most species identified in TCGA data are either not present at all, or are known contaminants rather than microbes residing within tumors.
submitted by: Istvan Albert
The complete sequence and comparative analysis of ape sex chromosomes | Nature (www.nature.com)
Complete sequence and comparison of Ape sex chromosomes.
submitted by: GenoMax
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