258: Correcting GC bias in metagenomes
No se pudo agregar al carrito
Add to Cart failed.
Error al Agregar a Lista de Deseos.
Error al eliminar de la lista de deseos.
Error al añadir a tu biblioteca
Error al seguir el podcast
Error al dejar de seguir el podcast
258: Correcting GC bias in metagenomes
-
Narrado por:
-
De:
Holcik L et al., Genomic GC bias correction improves species abundance estimation from metagenomic data. Nature Communications - GuaCAMOLE is an alignment-free algorithm that estimates and removes genomic GC-content-dependent sequencing bias to produce more accurate species abundance estimates from single metagenomic samples. Key terms: GC bias, metagenomics, species abundance, GuaCAMOLE, colorectal cancer.
Study Highlights:
GuaCAMOLE combines Kraken2/Bracken read assignment with per-taxon GC binning and a regularized least-squares estimator to infer GC-dependent sequencing efficiencies and bias-corrected abundances from a single sample. On simulations and mock communities across 28 library protocols it produced near-unbiased estimates and outperformed Bracken and MetaPhlAn4 when GC bias was present. Application to 3,435 gut microbiomes from 33 colorectal cancer studies revealed four distinct protocol-specific GC-bias shapes and systematic underestimation of GC-poor taxa. The tool also filters false-positive taxa by comparing observed and expected GC distributions and can apply inferred efficiencies to correct other tools' outputs.
Conclusion:
Per-sample GC-bias correction with GuaCAMOLE improves accuracy and comparability of metagenomic species abundance estimates across diverse protocols
Music:
Enjoy the music based on this article at the end of the episode.
Reference:
Holcik L., von Haeseler A., Pflug F. G. Genomic GC bias correction improves species abundance estimation from metagenomic data. Nature Communications. 2025;16:10523. https://doi.org/10.1038/s41467-025-65530-4
License:
This episode is based on an open-access article published under the Creative Commons Attribution 4.0 International License (CC BY 4.0) – https://creativecommons.org/licenses/by/4.0/
Support:
Base by Base – Stripe donations: https://donate.stripe.com/7sY4gz71B2sN3RWac5gEg00
Official website https://basebybase.com
On PaperCast Base by Base you’ll discover the latest in genomics, functional genomics, structural genomics, and proteomics.
Episode link: https://basebybase.castos.com/episodes/gc-bias-correction-metagenomics
Episode Slug: gc-bias-correction-metagenomics