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@article{pratas2014xs,
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@article{brouwer2016current,
title={Current opportunities and challenges of next generation sequencing (NGS) of DNA; determining health and disease},
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@article{cock2009sanger,
title={The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants},
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@article{price2017simulome,
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author={Price, Adam and Gibas, Cynthia},
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volume={33},
number={12},
pages={1876--1878},
year={2017},
publisher={Oxford University Press}
}
@article{huang2011art,
title={ART: a next-generation sequencing read simulator},
author={Huang, Weichun and Li, Leping and Myers, Jason R and Marth, Gabor T},
journal={Bioinformatics},
volume={28},
number={4},
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year={2011},
publisher={Oxford University Press}
}
@article{escalona2016comparison,
title={A comparison of tools for the simulation of genomic next-generation sequencing data},
author={Escalona, Merly and Rocha, Sara and Posada, David},
journal={Nature Reviews Genetics},
volume={17},
number={8},
pages={459},
year={2016},
publisher={Nature Publishing Group}
}
@article{baruzzo2017simulation,
title={Simulation-based comprehensive benchmarking of RNA-seq aligners},
author={Baruzzo, Giacomo and Hayer, Katharina E and Kim, Eun Ji and Di Camillo, Barbara and FitzGerald, Garret A and Grant, Gregory R},
journal={Nature methods},
volume={14},
number={2},
pages={135},
year={2017},
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}
@article{hosseini2016survey,
title={A survey on data compression methods for biological sequences},
author={Hosseini, Morteza and Pratas, Diogo and Pinho, Armando},
journal={Information},
volume={7},
number={4},
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year={2016},
publisher={Multidisciplinary Digital Publishing Institute}
}
@inproceedings{pratas2016efficient,
title={Efficient compression of genomic sequences},
author={Pratas, Diogo and Pinho, Armando J and Ferreira, Paulo JSG},
booktitle={2016 Data Compression Conference (DCC)},
pages={231--240},
year={2016},
organization={IEEE}
}
@article{hernaez2019genomic,
title={Genomic Data Compression},
author={Hernaez, Mikel and Pavlichin, Dmitri and Weissman, Tsachy and Ochoa, Idoia},
journal={Annual Review of Biomedical Data Science},
volume={2},
year={2019},
publisher={Annual Reviews}
}
@article{liu2017high,
title={High-speed and high-ratio referential genome compression},
author={Liu, Yuansheng and Peng, Hui and Wong, Limsoon and Li, Jinyan},
journal={Bioinformatics},
volume={33},
number={21},
pages={3364--3372},
year={2017},
publisher={Oxford University Press}
}
@article{ochoa2014idocomp,
title={iDoComp: a compression scheme for assembled genomes},
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journal={Bioinformatics},
volume={31},
number={5},
pages={626--633},
year={2014},
publisher={Oxford University Press}
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@article{deorowicz2015gdc,
title={GDC 2: Compression of large collections of genomes},
author={Deorowicz, Sebastian and Danek, Agnieszka and Niemiec, Marcin},
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year={2015},
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@article{hosseini2019ac,
title={AC: A Compression Tool for Amino Acid Sequences},
author={Hosseini, Morteza and Pratas, Diogo and Pinho, Armando J},
journal={Interdisciplinary Sciences: Computational Life Sciences},
pages={1--9},
year={2019},
publisher={Springer}
}
@article{nalbantoglu2010data,
title={Data compression concepts and algorithms and their applications to bioinformatics},
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@inproceedings{pratas2018compression,
title={Compression of amino acid sequences},
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booktitle={International Conference on Practical Applications of Computational Biology \& Bioinformatics},
pages={105--113},
year={2018},
organization={Springer}
}
@article{shen2016seqkit,
title={SeqKit: a cross-platform and ultrafast toolkit for FASTA/Q file manipulation},
author={Shen, Wei and Le, Shuai and Li, Yan and Hu, Fuquan},
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@article{droop2016fqtools,
title={fqtools: an efficient software suite for modern FASTQ file manipulation},
author={Droop, Alastair P},
journal={Bioinformatics},
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year={2016},
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@article{afgan2018galaxy,
title={The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update},
author={Afgan, Enis and Baker, Dannon and Batut, B{\'e}r{\'e}nice and Van Den Beek, Marius and Bouvier, Dave and {\v{C}}ech, Martin and Chilton, John and Clements, Dave and Coraor, Nate and Gr{\"u}ning, Bj{\"o}rn A and others},
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year={2018},
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@article{blankenberg2010manipulation,
title={Manipulation of FASTQ data with Galaxy},
author={Blankenberg, Daniel and Gordon, Assaf and Von Kuster, Gregory and Coraor, Nathan and Taylor, James and Nekrutenko, Anton and Galaxy Team},
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@article{goecks2010galaxy,
title={Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences},
author={Goecks, Jeremy and Nekrutenko, Anton and Taylor, James},
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}
@article{van2013fastq,
title={From FastQ data to high-confidence variant calls: the genome analysis toolkit best practices pipeline},
author={Van der Auwera, Geraldine A and Carneiro, Mauricio O and Hartl, Christopher and Poplin, Ryan and Del Angel, Guillermo and Levy-Moonshine, Ami and Jordan, Tadeusz and Shakir, Khalid and Roazen, David and Thibault, Joel and others},
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year={2013},
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@article{gordon2010fastx,
title={Fastx-toolkit},
author={Gordon, Assaf and Hannon, GJ and others},
journal={FASTQ/A short-reads preprocessing tools (unpublished) http://hannonlab. cshl. edu/fastx\_toolkit},
volume={5},
year={2010}
}