% MetaPathways workflow references. Full author lists from publisher-deposited Crossref metadata.
% Cite only applicable components; record actual software and database versions separately.

@article{mp_mp,
  author = {McLaughlin, Ryan J. and Liu, Tony X. and Altman, Tomer and Nallan, Aditi N. and Hahn, Aria S. and Anstett, Julia and Morgan-Lang, Connor and Konwar, Kishori M. and Hallam, Steven J.},
  title = {{MetaPathways v3.5: Modularity and Scalability Improvements for Pathway Inference from Environmental Genomes}},
  year = {2024},
  journal = {bioRxiv},
  doi = {10.1101/2024.06.04.597460},
  url = {https://github.com/hallamlab/MetaPathways},
}

@article{mp_nextflow,
  author = {Di Tommaso, Paolo and Chatzou, Maria and Floden, Evan W and Barja, Pablo Prieto and Palumbo, Emilio and Notredame, Cedric},
  title = {{Nextflow enables reproducible computational workflows}},
  year = {2017},
  journal = {Nature Biotechnology},
  volume = {35},
  number = {4},
  pages = {316--319},
  doi = {10.1038/nbt.3820},
  url = {https://www.nextflow.io/},
}

@article{mp_prodigal,
  author = {Hyatt, Doug and Chen, Gwo-Liang and LoCascio, Philip F and Land, Miriam L and Larimer, Frank W and Hauser, Loren J},
  title = {{Prodigal: prokaryotic gene recognition and translation initiation site identification}},
  year = {2010},
  journal = {BMC Bioinformatics},
  volume = {11},
  number = {1},
  pages = {119},
  doi = {10.1186/1471-2105-11-119},
  url = {https://github.com/hyattpd/Prodigal},
}

@article{mp_last,
  author = {Kiełbasa, Szymon M. and Wan, Raymond and Sato, Kengo and Horton, Paul and Frith, Martin C.},
  title = {{Adaptive seeds tame genomic sequence comparison}},
  year = {2011},
  journal = {Genome Research},
  volume = {21},
  number = {3},
  pages = {487--493},
  doi = {10.1101/gr.113985.110},
  url = {https://gitlab.com/mcfrith/last},
}

@article{mp_blast,
  author = {Camacho, Christiam and Coulouris, George and Avagyan, Vahram and Ma, Ning and Papadopoulos, Jason and Bealer, Kevin and Madden, Thomas L},
  title = {{BLAST+: architecture and applications}},
  year = {2009},
  journal = {BMC Bioinformatics},
  volume = {10},
  number = {1},
  pages = {421},
  doi = {10.1186/1471-2105-10-421},
  url = {https://blast.ncbi.nlm.nih.gov/},
}

@article{mp_nhmmer,
  author = {Wheeler, Travis J. and Eddy, Sean R.},
  title = {{nhmmer: DNA homology search with profile HMMs}},
  year = {2013},
  journal = {Bioinformatics},
  volume = {29},
  number = {19},
  pages = {2487--2489},
  doi = {10.1093/bioinformatics/btt403},
  url = {http://hmmer.org/},
}

@article{mp_infernal,
  author = {Nawrocki, Eric P. and Eddy, Sean R.},
  title = {{Infernal 1.1: 100-fold faster RNA homology searches}},
  year = {2013},
  journal = {Bioinformatics},
  volume = {29},
  number = {22},
  pages = {2933--2935},
  doi = {10.1093/bioinformatics/btt509},
  url = {http://eddylab.org/infernal/},
}

@article{mp_trnascan,
  author = {Chan, Patricia P and Lin, Brian Y and Mak, Allysia J and Lowe, Todd M},
  title = {{tRNAscan-SE 2.0: improved detection and functional classification of transfer RNA genes}},
  year = {2021},
  journal = {Nucleic Acids Research},
  volume = {49},
  number = {16},
  pages = {9077--9096},
  doi = {10.1093/nar/gkab688},
  url = {https://trna.ucsc.edu/tRNAscan-SE/},
}

@article{mp_pybedtools,
  author = {Dale, Ryan K. and Pedersen, Brent S. and Quinlan, Aaron R.},
  title = {{Pybedtools: a flexible Python library for manipulating genomic datasets and annotations}},
  year = {2011},
  journal = {Bioinformatics},
  volume = {27},
  number = {24},
  pages = {3423--3424},
  doi = {10.1093/bioinformatics/btr539},
  url = {https://github.com/daler/pybedtools},
}

@article{mp_bedtools,
  author = {Quinlan, Aaron R. and Hall, Ira M.},
  title = {{BEDTools: a flexible suite of utilities for comparing genomic features}},
  year = {2010},
  journal = {Bioinformatics},
  volume = {26},
  number = {6},
  pages = {841--842},
  doi = {10.1093/bioinformatics/btq033},
  url = {https://github.com/arq5x/bedtools2},
}

@article{mp_coverm,
  author = {Aroney, Samuel T N and Newell, Rhys J P and Nissen, Jakob N and Camargo, Antonio Pedro and Tyson, Gene W and Woodcroft, Ben J},
  title = {{CoverM: read alignment statistics for metagenomics}},
  year = {2025},
  journal = {Bioinformatics},
  volume = {41},
  number = {4},
  pages = {btaf147},
  doi = {10.1093/bioinformatics/btaf147},
  url = {https://github.com/wwood/CoverM},
}

@article{mp_samtools,
  author = {Danecek, Petr and Bonfield, James K and Liddle, Jennifer and Marshall, John and Ohan, Valeriu and Pollard, Martin O and Whitwham, Andrew and Keane, Thomas and McCarthy, Shane A and Davies, Robert M and Li, Heng},
  title = {{Twelve years of SAMtools and BCFtools}},
  year = {2021},
  journal = {GigaScience},
  volume = {10},
  number = {2},
  pages = {giab008},
  doi = {10.1093/gigascience/giab008},
  url = {https://www.htslib.org/},
}

@article{mp_featurecounts,
  author = {Liao, Yang and Smyth, Gordon K. and Shi, Wei},
  title = {{featureCounts: an efficient general purpose program for assigning sequence reads to genomic features}},
  year = {2014},
  journal = {Bioinformatics},
  volume = {30},
  number = {7},
  pages = {923--930},
  doi = {10.1093/bioinformatics/btt656},
  url = {https://subread.sourceforge.net/},
}

@article{mp_ptools,
  author = {Karp, Peter D. and Latendresse, Mario and Paley, Suzanne M. and Krummenacker, Markus and Ong, Quang D. and Billington, Richard and Kothari, Anamika and Weaver, Daniel and Lee, Thomas and Subhraveti, Pallavi and Spaulding, Aaron and Fulcher, Carol and Keseler, Ingrid M. and Caspi, Ron},
  title = {{Pathway Tools version 19.0 update: software for pathway/genome informatics and systems biology}},
  year = {2016},
  journal = {Briefings in Bioinformatics},
  volume = {17},
  number = {5},
  pages = {877--890},
  doi = {10.1093/bib/bbv079},
  url = {https://www.pathwaytools.org/},
}

@article{mp_minimap2,
  author = {Li, Heng},
  title = {{Minimap2: pairwise alignment for nucleotide sequences}},
  year = {2018},
  journal = {Bioinformatics},
  volume = {34},
  number = {18},
  pages = {3094--3100},
  doi = {10.1093/bioinformatics/bty191},
  url = {https://github.com/lh3/minimap2},
}

@article{mp_bwa,
  author = {Li, Heng and Durbin, Richard},
  title = {{Fast and accurate short read alignment with Burrows–Wheeler transform}},
  year = {2009},
  journal = {Bioinformatics},
  volume = {25},
  number = {14},
  pages = {1754--1760},
  doi = {10.1093/bioinformatics/btp324},
  url = {https://github.com/lh3/bwa},
}

@article{mp_strobealign,
  author = {Sahlin, Kristoffer},
  title = {{Strobealign: flexible seed size enables ultra-fast and accurate read alignment}},
  year = {2022},
  journal = {Genome Biology},
  volume = {23},
  number = {1},
  pages = {260},
  doi = {10.1186/s13059-022-02831-7},
  url = {https://github.com/ksahlin/strobealign},
}

@article{mp_apptainer,
  author = {Kurtzer, Gregory M. and Sochat, Vanessa and Bauer, Michael W.},
  title = {{Singularity: Scientific containers for mobility of compute}},
  year = {2017},
  journal = {PLOS ONE},
  volume = {12},
  number = {5},
  pages = {e0177459},
  doi = {10.1371/journal.pone.0177459},
  url = {https://github.com/apptainer/apptainer#citing-apptainer},
}

@inproceedings{mp_slurm,
  author = {Yoo, Andy B. and Jette, Morris A. and Grondona, Mark},
  title = {{SLURM: Simple Linux Utility for Resource Management}},
  year = {2003},
  booktitle = {Job Scheduling Strategies for Parallel Processing},
  series = {Lecture Notes in Computer Science},
  volume = {2862},
  pages = {44--60},
  doi = {10.1007/10968987_3},
  url = {https://slurm.schedmd.com/},
}

@article{mp_bioconda,
  author = {{The Bioconda Team} and Grüning, Björn and Dale, Ryan and Sjödin, Andreas and Chapman, Brad A. and Rowe, Jillian and Tomkins-Tinch, Christopher H. and Valieris, Renan and Köster, Johannes},
  title = {{Bioconda: sustainable and comprehensive software distribution for the life sciences}},
  year = {2018},
  journal = {Nature Methods},
  volume = {15},
  number = {7},
  pages = {475--476},
  doi = {10.1038/s41592-018-0046-7},
  url = {https://bioconda.github.io/},
}

@inproceedings{mp_pandas,
  author = {McKinney, Wes},
  title = {{Data Structures for Statistical Computing in Python}},
  year = {2010},
  booktitle = {Proceedings of the Python in Science Conference},
  pages = {56--61},
  doi = {10.25080/majora-92bf1922-00a},
  url = {https://pandas.pydata.org/},
}

@article{mp_numpy,
  author = {Harris, Charles R. and Millman, K. Jarrod and van der Walt, Stéfan J. and Gommers, Ralf and Virtanen, Pauli and Cournapeau, David and Wieser, Eric and Taylor, Julian and Berg, Sebastian and Smith, Nathaniel J. and Kern, Robert and Picus, Matti and Hoyer, Stephan and van Kerkwijk, Marten H. and Brett, Matthew and Haldane, Allan and del Río, Jaime Fernández and Wiebe, Mark and Peterson, Pearu and Gérard-Marchant, Pierre and Sheppard, Kevin and Reddy, Tyler and Weckesser, Warren and Abbasi, Hameer and Gohlke, Christoph and Oliphant, Travis E.},
  title = {{Array programming with NumPy}},
  year = {2020},
  journal = {Nature},
  volume = {585},
  number = {7825},
  pages = {357--362},
  doi = {10.1038/s41586-020-2649-2},
  url = {https://numpy.org/},
}

@article{mp_scipy,
  author = {Virtanen, Pauli and Gommers, Ralf and Oliphant, Travis E. and Haberland, Matt and Reddy, Tyler and Cournapeau, David and Burovski, Evgeni and Peterson, Pearu and Weckesser, Warren and Bright, Jonathan and van der Walt, Stéfan J. and Brett, Matthew and Wilson, Joshua and Millman, K. Jarrod and Mayorov, Nikolay and Nelson, Andrew R. J. and Jones, Eric and Kern, Robert and Larson, Eric and Carey, C J and Polat, İlhan and Feng, Yu and Moore, Eric W. and VanderPlas, Jake and Laxalde, Denis and Perktold, Josef and Cimrman, Robert and Henriksen, Ian and Quintero, E. A. and Harris, Charles R. and Archibald, Anne M. and Ribeiro, Antônio H. and Pedregosa, Fabian and van Mulbregt, Paul and {SciPy 1.0 Contributors} and Vijaykumar, Aditya and Bardelli, Alessandro Pietro and Rothberg, Alex and Hilboll, Andreas and Kloeckner, Andreas and Scopatz, Anthony and Lee, Antony and Rokem, Ariel and Woods, C. Nathan and Fulton, Chad and Masson, Charles and Häggström, Christian and Fitzgerald, Clark and Nicholson, David A. and Hagen, David R. and Pasechnik, Dmitrii V. and Olivetti, Emanuele and Martin, Eric and Wieser, Eric and Silva, Fabrice and Lenders, Felix and Wilhelm, Florian and Young, G. and Price, Gavin A. and Ingold, Gert-Ludwig and Allen, Gregory E. and Lee, Gregory R. and Audren, Hervé and Probst, Irvin and Dietrich, Jörg P. and Silterra, Jacob and Webber, James T and Slavič, Janko and Nothman, Joel and Buchner, Johannes and Kulick, Johannes and Schönberger, Johannes L. and de Miranda Cardoso, José Vinícius and Reimer, Joscha and Harrington, Joseph and Rodríguez, Juan Luis Cano and Nunez-Iglesias, Juan and Kuczynski, Justin and Tritz, Kevin and Thoma, Martin and Newville, Matthew and Kümmerer, Matthias and Bolingbroke, Maximilian and Tartre, Michael and Pak, Mikhail and Smith, Nathaniel J. and Nowaczyk, Nikolai and Shebanov, Nikolay and Pavlyk, Oleksandr and Brodtkorb, Per A. and Lee, Perry and McGibbon, Robert T. and Feldbauer, Roman and Lewis, Sam and Tygier, Sam and Sievert, Scott and Vigna, Sebastiano and Peterson, Stefan and More, Surhud and Pudlik, Tadeusz and Oshima, Takuya and Pingel, Thomas J. and Robitaille, Thomas P. and Spura, Thomas and Jones, Thouis R. and Cera, Tim and Leslie, Tim and Zito, Tiziano and Krauss, Tom and Upadhyay, Utkarsh and Halchenko, Yaroslav O. and Vázquez-Baeza, Yoshiki},
  title = {{SciPy 1.0: fundamental algorithms for scientific computing in Python}},
  year = {2020},
  journal = {Nature Methods},
  volume = {17},
  number = {3},
  pages = {261--272},
  doi = {10.1038/s41592-019-0686-2},
  url = {https://scipy.org/},
}

@article{mp_pyfastx,
  author = {Du, Lianming and Liu, Qin and Fan, Zhenxin and Tang, Jie and Zhang, Xiuyue and Price, Megan and Yue, Bisong and Zhao, Kelei},
  title = {{Pyfastx: a robust Python package for fast random access to sequences from plain and gzipped FASTA/Q files}},
  year = {2021},
  journal = {Briefings in Bioinformatics},
  volume = {22},
  number = {4},
  pages = {bbaa368},
  doi = {10.1093/bib/bbaa368},
  url = {https://github.com/lmdu/pyfastx},
}

@article{mp_cython,
  author = {Behnel, Stefan and Bradshaw, Robert and Citro, Craig and Dalcin, Lisandro and Seljebotn, Dag Sverre and Smith, Kurt},
  title = {{Cython: The Best of Both Worlds}},
  year = {2011},
  journal = {Computing in Science \& Engineering},
  volume = {13},
  number = {2},
  pages = {31--39},
  doi = {10.1109/mcse.2010.118},
  url = {https://cython.org/},
}

@article{mp_uniprot,
  author = {{The UniProt Consortium} and Bateman, Alex and Martin, Maria-Jesus and Orchard, Sandra and Magrane, Michele and Ahmad, Shadab and Alpi, Emanuele and Bowler-Barnett, Emily H and Britto, Ramona and Bye-A-Jee, Hema and Cukura, Austra and Denny, Paul and Dogan, Tunca and Ebenezer, ThankGod and Fan, Jun and Garmiri, Penelope and da Costa Gonzales, Leonardo Jose and Hatton-Ellis, Emma and Hussein, Abdulrahman and Ignatchenko, Alexandr and Insana, Giuseppe and Ishtiaq, Rizwan and Joshi, Vishal and Jyothi, Dushyanth and Kandasaamy, Swaathi and Lock, Antonia and Luciani, Aurelien and Lugaric, Marija and Luo, Jie and Lussi, Yvonne and MacDougall, Alistair and Madeira, Fabio and Mahmoudy, Mahdi and Mishra, Alok and Moulang, Katie and Nightingale, Andrew and Pundir, Sangya and Qi, Guoying and Raj, Shriya and Raposo, Pedro and Rice, Daniel L and Saidi, Rabie and Santos, Rafael and Speretta, Elena and Stephenson, James and Totoo, Prabhat and Turner, Edward and Tyagi, Nidhi and Vasudev, Preethi and Warner, Kate and Watkins, Xavier and Zaru, Rossana and Zellner, Hermann and Bridge, Alan J and Aimo, Lucila and Argoud-Puy, Ghislaine and Auchincloss, Andrea H and Axelsen, Kristian B and Bansal, Parit and Baratin, Delphine and Batista Neto, Teresa M and Blatter, Marie-Claude and Bolleman, Jerven T and Boutet, Emmanuel and Breuza, Lionel and Gil, Blanca Cabrera and Casals-Casas, Cristina and Echioukh, Kamal Chikh and Coudert, Elisabeth and Cuche, Beatrice and de Castro, Edouard and Estreicher, Anne and Famiglietti, Maria L and Feuermann, Marc and Gasteiger, Elisabeth and Gaudet, Pascale and Gehant, Sebastien and Gerritsen, Vivienne and Gos, Arnaud and Gruaz, Nadine and Hulo, Chantal and Hyka-Nouspikel, Nevila and Jungo, Florence and Kerhornou, Arnaud and Le Mercier, Philippe and Lieberherr, Damien and Masson, Patrick and Morgat, Anne and Muthukrishnan, Venkatesh and Paesano, Salvo and Pedruzzi, Ivo and Pilbout, Sandrine and Pourcel, Lucille and Poux, Sylvain and Pozzato, Monica and Pruess, Manuela and Redaschi, Nicole and Rivoire, Catherine and Sigrist, Christian J A and Sonesson, Karin and Sundaram, Shyamala and Wu, Cathy H and Arighi, Cecilia N and Arminski, Leslie and Chen, Chuming and Chen, Yongxing and Huang, Hongzhan and Laiho, Kati and McGarvey, Peter and Natale, Darren A and Ross, Karen and Vinayaka, C R and Wang, Qinghua and Wang, Yuqi and Zhang, Jian},
  title = {{UniProt: the Universal Protein Knowledgebase in 2023}},
  year = {2023},
  journal = {Nucleic Acids Research},
  volume = {51},
  number = {D1},
  pages = {D523--D531},
  doi = {10.1093/nar/gkac1052},
  url = {https://www.uniprot.org/},
}

@article{mp_uniref,
  author = {Suzek, Baris E. and Huang, Hongzhan and McGarvey, Peter and Mazumder, Raja and Wu, Cathy H.},
  title = {{UniRef: comprehensive and non-redundant UniProt reference clusters}},
  year = {2007},
  journal = {Bioinformatics},
  volume = {23},
  number = {10},
  pages = {1282--1288},
  doi = {10.1093/bioinformatics/btm098},
  url = {https://www.uniprot.org/uniref},
}

@article{mp_cazy,
  author = {Drula, Elodie and Garron, Marie-Line and Dogan, Suzan and Lombard, Vincent and Henrissat, Bernard and Terrapon, Nicolas},
  title = {{The carbohydrate-active enzyme database: functions and literature}},
  year = {2022},
  journal = {Nucleic Acids Research},
  volume = {50},
  number = {D1},
  pages = {D571--D577},
  doi = {10.1093/nar/gkab1045},
  url = {https://www.cazy.org/},
}

@article{mp_eggnog,
  author = {Huerta-Cepas, Jaime and Szklarczyk, Damian and Heller, Davide and Hernández-Plaza, Ana and Forslund, Sofia K and Cook, Helen and Mende, Daniel R and Letunic, Ivica and Rattei, Thomas and Jensen, Lars J and von Mering, Christian and Bork, Peer},
  title = {{eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses}},
  year = {2019},
  journal = {Nucleic Acids Research},
  volume = {47},
  number = {D1},
  pages = {D309--D314},
  doi = {10.1093/nar/gky1085},
  url = {http://eggnog.embl.de/},
}

@article{mp_silva,
  author = {Quast, Christian and Pruesse, Elmar and Yilmaz, Pelin and Gerken, Jan and Schweer, Timmy and Yarza, Pablo and Peplies, Jörg and Glöckner, Frank Oliver},
  title = {{The SILVA ribosomal RNA gene database project: improved data processing and web-based tools}},
  year = {2013},
  journal = {Nucleic Acids Research},
  volume = {41},
  number = {D1},
  pages = {D590--D596},
  doi = {10.1093/nar/gks1219},
  url = {https://www.arb-silva.de/},
}

@article{mp_ncbi,
  author = {Schoch, Conrad L and Ciufo, Stacy and Domrachev, Mikhail and Hotton, Carol L and Kannan, Sivakumar and Khovanskaya, Rogneda and Leipe, Detlef and Mcveigh, Richard and O’Neill, Kathleen and Robbertse, Barbara and Sharma, Shobha and Soussov, Vladimir and Sullivan, John P and Sun, Lu and Turner, Seán and Karsch-Mizrachi, Ilene},
  title = {{NCBI Taxonomy: a comprehensive update on curation, resources and tools}},
  year = {2020},
  journal = {Database},
  volume = {2020},
  pages = {baaa062},
  doi = {10.1093/database/baaa062},
  url = {https://www.ncbi.nlm.nih.gov/taxonomy},
}

@article{mp_enzyme,
  author = {Bairoch, A.},
  title = {{The ENZYME database in 2000}},
  year = {2000},
  journal = {Nucleic Acids Research},
  volume = {28},
  number = {1},
  pages = {304--305},
  doi = {10.1093/nar/28.1.304},
  url = {https://enzyme.expasy.org/},
}

@article{mp_metacyc,
  author = {Caspi, Ron and Billington, Richard and Keseler, Ingrid M and Kothari, Anamika and Krummenacker, Markus and Midford, Peter E and Ong, Wai Kit and Paley, Suzanne and Subhraveti, Pallavi and Karp, Peter D},
  title = {{The MetaCyc database of metabolic pathways and enzymes - a 2019 update}},
  year = {2020},
  journal = {Nucleic Acids Research},
  volume = {48},
  number = {D1},
  pages = {D445--D453},
  doi = {10.1093/nar/gkz862},
  url = {https://metacyc.org/},
}