Mark F. Bennett | Searcharxiv

arXiv2026

SVPLEX: A Nextflow Pipeline for Cohort-level Structural Variant Calling

SVPLEX is a Nextflow pipeline for cohort-level structural variant detection from short-read whole-genome sequencing data. The pipeline implements six different structural variant callers with different strengths and weaknesses, integrating different levels of evidence for SVs, and generates a merged consensus callset across the analysis cohort. Callset filtering is achieved by leveraging consensus among multiple individual callers and by ensuring that deletion and duplication calls are supported by observable changes in read depth. The output merged cohort SV callset can then be used to assess cohort-specific variation, remove technical artefacts, and serve as input for rare disease variant prioritisation workflows. SVPLEX is user-friendly, reproducible, scalable, and can be executed flexibly on either a local workstation, a high-performance compute (HPC) cluster, or deployed on cloud infrastructure. The required inputs are alignment files for the cohort of interest, and the output is a single merged cohort structural variant VCF. SVPLEX is available on GitHub (bahlolab/SVPLEX) and is licensed under the MIT open-source licence.

q-bio.GN↗

arXiv2013

Stochastic gravitational wave background from hydrodynamic turbulence in differentially rotating neutron stars

Hydrodynamic turbulence driven by crust-core differential rotation imposes a fundamental noise floor on gravitational wave observations of neutron stars. The gravitational wave emission peaks at the Kolmogorov decoherence frequency which, for reasonable values of the crust-core shear, ΔΩ, occurs near the most sensitive part of the frequency band for ground-based, long-baseline interferometers. We calculate the energy density spectrum of the stochastic gravitational wave background from a cosmological population of turbulent neutron stars generalising previous calculations for individual sources. The spectrum resembles a piecewise power law, Ω_{gw}(ν)=Ω_αν^α, with α=-1 and 7 above and below the decoherence frequency respectively, and its normalisation scales as Ω_α\propto(ΔΩ)^{7}. Non-detection of a stochastic signal by Initial LIGO implies an upper limit on ΔΩand hence by implication on the internal relaxation time-scale for the crust and core to come into co-rotation, τ_{d}=ΔΩ/\dotΩ, where \dotΩ is the observed electromagnetic spin-down rate, with τ_{d}\lesssim 10^{7} yr for accreting millisecond pulsars and τ_{d}\lesssim 10^{5} yr for radio-loud pulsars. Target limits on τ_{d} are also estimated for future detectors, namely Advanced LIGO and the Einstein Telescope, and are found to be astrophysically interesting.

astro-ph.HE↗