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Giulio Formenti, Linelle Ann L. Abueg, Angelo Brajuka, Nadolina Brajuka, Cristóbal Gallardo Alba, Alice Maria Giani, Olivier D. Fedrigo, Erich David Jarvis
MOTIVATION: With the current pace at which reference genomes are being produced, the availability of tools that can reliably and efficiently generate genome assembly summary statistics has become critical. Additionally, with the emergence of new algorithms and data types, tools that can improve the quality of existing assemblies through automated and manual curation are required. RESULTS: We sought to address both these needs by developing gfastats, as part of the Vertebrate Genomes Project (VGP) effort to generate high-quality reference genomes at scale. Gfastats is a standalone tool to compute assembly summary statistics and manipulate assembly sequences in FASTA, FASTQ or GFA [.gz] format. Gfastats stores assembly sequences internally in a GFA-like format. This feature allows gfastats to seamlessly convert FAST* to and from GFA [.gz] files. Gfastats can also build an assembly graph that can in turn be used to manipulate the underlying sequences following instructions provided by the user, while simultaneously generating key metrics for the new sequences. AVAILABILITY AND IMPLEMENTATION: Gfastats is implemented in C++. Precompiled releases (Linux, MacOS, Windows) and commented source code for gfastats are available under MIT licence at https://github.com/vgl-hub/gfastats. Examples of how to run gfastats are provided in the GitHub. Gfastats is also available in Bioconda, in Galaxy (https://assembly.usegalaxy.eu) and as a MultiQC module (https://github.com/ewels/MultiQC). An automated test workflow is available to ensure consistency of software updates. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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Formenti, G., Abueg, L. A. L., Brajuka, A., Brajuka, N., Alba, C. G., Giani, A. M., Fedrigo, O. D., & Jarvis, E. D. (2022). Gfastats: conversion, evaluation and manipulation of genome sequences using assembly graphs. Bioinformatics, 38(17), 4214–4216. https://doi.org/10.1093/bioinformatics/btac460
Formenti, Giulio, et al. "Gfastats: conversion, evaluation and manipulation of genome sequences using assembly graphs." Bioinformatics, vol. 38, no. 17, 2022, pp. 4214–4216, https://doi.org/10.1093/bioinformatics/btac460.
Formenti, Giulio, Linelle Ann L. Abueg, Angelo Brajuka, Nadolina Brajuka, Cristóbal Gallardo Alba, Alice Maria Giani, Olivier D. Fedrigo, and Erich David Jarvis. "Gfastats: conversion, evaluation and manipulation of genome sequences using assembly graphs." Bioinformatics 38, no. 17 (2022): 4214–4216. https://doi.org/10.1093/bioinformatics/btac460.
Formenti G., Abueg L. A. L., Brajuka A. [и др.] Gfastats: conversion, evaluation and manipulation of genome sequences using assembly graphs // Bioinformatics. — 2022. — Vol. 38, № 17. — P. 4214–4216. — URL: https://doi.org/10.1093/bioinformatics/btac460
@article{formenti2022gfastats,
title = {{Gfastats: conversion, evaluation and manipulation of genome sequences using assembly graphs}},
author = {Giulio Formenti and Linelle Ann L. Abueg and Angelo Brajuka and Nadolina Brajuka and Cristóbal Gallardo Alba and Alice Maria Giani and Olivier D. Fedrigo and Erich David Jarvis},
journal = {Bioinformatics},
year = {2022},
volume = {38},
number = {17},
pages = {4214--4216},
doi = {10.1093/bioinformatics/btac460},
url = {https://doi.org/10.1093/bioinformatics/btac460}
}TY - JOUR AU - Formenti, Giulio AU - Abueg, Linelle Ann L. AU - Brajuka, Angelo AU - Brajuka, Nadolina AU - Alba, Cristóbal Gallardo AU - Giani, Alice Maria AU - Fedrigo, Olivier D. AU - Jarvis, Erich David TI - Gfastats: conversion, evaluation and manipulation of genome sequences using assembly graphs JO - Bioinformatics VL - 38 IS - 17 SP - 4214 EP - 4216 PY - 2022 DA - 2022/07/07 DO - 10.1093/bioinformatics/btac460 UR - https://doi.org/10.1093/bioinformatics/btac460 ER -
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