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Faster Sorting of Aligned DNA-Read Files

Abstract (Expand)

In the analysis of DNA sequencing data for finding disease causing mutations, to understand evolutionary relationships between species, and to find variants, DNA-Reads are compared to a reference genome. … A reference genome is a representative example for a set of genes of a species. Sorting these aligned DNA-Reads by their position within the reference sequence is a crucial step in many of these downstream analyses. SAMtools sort, a widely used tool, performs external memory sorting of aligned DNA-Reads stored in the BAM format (Binary Alignment Map). This format allows for compressed storage of alignment data. SAMtools sort provides the most comprehensive set of features while exhibiting demonstrably faster execution times than its open source alternatives. In this work, we analyze SAMtools sort for sorting BAM files and propose methods to reduce its runtime. We divide the analysis into three parts: management of temporary files, compression, and input/output (IO). For the management of temporary files, we find that the maximum number of temporary files SAMtools sort can open concurrently is lower than the maximum number of open files permitted by the operating system. This results in an unnecessarily high number of merges of temporary files into larger temporary files, introducing overhead as SAMtools sort performs extra write and compression operations. To overcome this, we propose a dynamic limit for the number of temporary files, adapting to the operating system’s soft limit for open files. For compression, we test seven different libraries for compatible compression and a range of compression levels, identifying options that offer faster compression and result in a speedup of up to five times in single-threaded execution of SAMtools sort. For IO, we demonstrate that a minimal level of compression avoids IO overhead, thereby reducing the runtime of SAMtools sort compared to uncompressed output. However, we also show that uncompressed output can be used in the pipelining of SAMtools commands to reduce the runtime of subsequent SAMtools commands. Our proposed modifications to SAMtools sort and user behavior have the potential to achieve speedups of up to 6. This represents an important contribution to the field of bioinformatics, considering the widespread adoption of SAMtools sort evidenced by its over 5,000 citations and over 5.1 million downloads through Bioconda.

Authors: Dominik Siebelt, Lukas Hübner, Alexandros Stamatakis

Date Published: 3rd Jun 2024

Publication Type: Bachelor's Thesis

SN 2020pvb: A Type IIn-P supernova with a precursor outburst

Abstract

Not specified

Authors: N. Elias-Rosa, S. J. Brennan, S. Benetti, E. Cappellaro, A. Pastorello, A. Kozyreva, P. Lundqvist, M. Fraser, J. P. Anderson, Y. -Z. Cai, T. -W. Chen, M. Dennefeld, M. Gromadzki, C. P. Gutiérrez, N. Ihanec, C. Inserra, E. Kankare, R. Kotak, S. Mattila, S. Moran, T. E. Müller-Bravo, P. J. Pessi, G. Pignata, A. Reguitti, T. M. Reynolds, S. J. Smartt, K. Smith, L. Tartaglia, G. Valerin, T. de Boer, K. Chambers, A. Gal-Yam, H. Gao, S. Geier, P. A. Mazzali, M. Nicholl, F. Ragosta, A. Rest, O. Yaron, D. R. Young

Date Published: 1st Jun 2024

Publication Type: Journal

Type Ia supernova explosion models are inherently multidimensional

Abstract

Not specified

Authors: Rüdiger Pakmor, Ivo R. Seitenzahl, Ashley J. Ruiter, Stuart A. Sim, Friedrich K. Röpke, Stefan Taubenberger, Rebekka Bieri, Stéphane Blondin

Date Published: 1st Jun 2024

Publication Type: Journal

Performance of high-order Godunov-type methods in simulations of astrophysical low Mach number flows

Abstract

Not specified

Authors: G. Leidi, R. Andrassy, W. Barsukow, J. Higl, P. V. F. Edelmann, F. K. Röpke

Date Published: 1st Jun 2024

Publication Type: Journal

H  i discs of L* galaxies as probes of the baryonic physics of galaxy evolution

Abstract (Expand)

ABSTRACT Understanding what shapes the cold gas component of galaxies, which both provides the fuel for star formation and is strongly affected by the subsequent stellar feedback, is a crucial step …eedback, is a crucial step towards a better understanding of galaxy evolution. Here, we analyse the H i properties of a sample of 46 Milky Way halo-mass galaxies, drawn from cosmological simulations (EMP-Pathfinder and Firebox). This set of simulations comprises galaxies evolved self-consistently across cosmic time with different baryonic sub-grid physics: three different star formation models [constant star formation efficiency (SFE) with different star formation eligibility criteria, and an environmentally dependent, turbulence-based SFE] and two different feedback prescriptions, where only one sub-sample includes early stellar feedback. We use these simulations to assess the impact of different baryonic physics on the H i content of galaxies. We find that the galaxy-wide H i properties agree with each other and with observations. However, differences appear for small-scale properties. The thin H i discs observed in the local universe are only reproduced with a turbulence-dependent SFE and/or early stellar feedback. Furthermore, we find that the morphology of H i discs is particularly sensitive to the different physics models: galaxies simulated with a turbulence-based SFE have discs that are smoother and more rotationally symmetric, compared to those simulated with a constant SFE; galaxies simulated with early stellar feedback have more regular discs than supernova-feedback-only galaxies. We find that the rotational asymmetry of the H i discs depends most strongly on the underlying physics model, making this a promising observable for understanding the physics responsible for shaping the interstellar medium of galaxies.

Authors: Jindra Gensior, Robert Feldmann, Marta Reina-Campos, Sebastian Trujillo-Gomez, Lucio Mayer, Benjamin W Keller, Andrew Wetzel, J M Diederik Kruijssen, Philip F Hopkins, Jorge Moreno

Date Published: 1st Jun 2024

Publication Type: Journal

Pre-supernova evolution and final fate of stellar mergers and accretors of binary mass transfer

Abstract

Not specified

Authors: F. R. N. Schneider, Ph. Podsiadlowski, E. Laplace

Date Published: 1st Jun 2024

Publication Type: Journal

Prediction of diagnosis and diastolic filling pressure by AI-enhanced cardiac MRI: a modelling study of hospital data

Abstract

Not specified

Authors: David Hermann Lehmann, Bruna Gomes, Niklas Vetter, Olivia Braun, Ali Amr, Thomas Hilbel, Jens Müller, Ulrich Köthe, Christoph Reich, Elham Kayvanpour, Farbod Sedaghat-Hamedani, Manuela Meder, Jan Haas, Euan Ashley, Wolfgang Rottbauer, Dominik Felbel, Raffi Bekeredjian, Heiko Mahrholdt, Andreas Keller, Peter Ong, Andreas Seitz, Hauke Hund, Nicolas Geis, Florian André, Sandy Engelhardt, Hugo A Katus, Norbert Frey, Vincent Heuveline, Benjamin Meder

Date Published: 1st Jun 2024

Publication Type: Journal

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