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Haplotype-Phased Synthetic Long Reads from Short-Read Sequencing.
PLoS One. 2016 Jan 20;11(1):e0147229. doi: 10.1371/journal.pone.0147229. eCollection 2016.
PLoS One. 2016.
PMID: 26789840
Free PMC article.
Large-scale sequence comparisons with sourmash.
Pierce NT, Irber L, Reiter T, Brooks P, Brown CT.
Pierce NT, et al.
F1000Res. 2019 Jul 4;8:1006. doi: 10.12688/f1000research.19675.1. eCollection 2019.
F1000Res. 2019.
PMID: 31508216
Free PMC article.
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Streamlining data-intensive biology with workflow systems.
Reiter T, Brooks PT, Irber L, Joslin SEK, Reid CM, Scott C, Brown CT, Pierce-Ward NT.
Reiter T, et al.
Gigascience. 2021 Jan 13;10(1):giaa140. doi: 10.1093/gigascience/giaa140.
Gigascience. 2021.
PMID: 33438730
Free PMC article.
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The khmer software package: enabling efficient nucleotide sequence analysis.
Crusoe MR, Alameldin HF, Awad S, Boucher E, Caldwell A, Cartwright R, Charbonneau A, Constantinides B, Edvenson G, Fay S, Fenton J, Fenzl T, Fish J, Garcia-Gutierrez L, Garland P, Gluck J, González I, Guermond S, Guo J, Gupta A, Herr JR, Howe A, Hyer A, Härpfer A, Irber L, Kidd R, Lin D, Lippi J, Mansour T, McA'Nulty P, McDonald E, Mizzi J, Murray KD, Nahum JR, Nanlohy K, Nederbragt AJ, Ortiz-Zuazaga H, Ory J, Pell J, Pepe-Ranney C, Russ ZN, Schwarz E, Scott C, Seaman J, Sievert S, Simpson J, Skennerton CT, Spencer J, Srinivasan R, Standage D, Stapleton JA, Steinman SR, Stein J, Taylor B, Trimble W, Wiencko HL, Wright M, Wyss B, Zhang Q, Zyme E, Brown CT.
Crusoe MR, et al.
F1000Res. 2015 Sep 25;4:900. doi: 10.12688/f1000research.6924.1. eCollection 2015.
F1000Res. 2015.
PMID: 26535114
Free PMC article.
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Critical Assessment of Metagenome Interpretation: the second round of challenges.
Meyer F, Fritz A, Deng ZL, Koslicki D, Lesker TR, Gurevich A, Robertson G, Alser M, Antipov D, Beghini F, Bertrand D, Brito JJ, Brown CT, Buchmann J, Buluç A, Chen B, Chikhi R, Clausen PTLC, Cristian A, Dabrowski PW, Darling AE, Egan R, Eskin E, Georganas E, Goltsman E, Gray MA, Hansen LH, Hofmeyr S, Huang P, Irber L, Jia H, Jørgensen TS, Kieser SD, Klemetsen T, Kola A, Kolmogorov M, Korobeynikov A, Kwan J, LaPierre N, Lemaitre C, Li C, Limasset A, Malcher-Miranda F, Mangul S, Marcelino VR, Marchet C, Marijon P, Meleshko D, Mende DR, Milanese A, Nagarajan N, Nissen J, Nurk S, Oliker L, Paoli L, Peterlongo P, Piro VC, Porter JS, Rasmussen S, Rees ER, Reinert K, Renard B, Robertsen EM, Rosen GL, Ruscheweyh HJ, Sarwal V, Segata N, Seiler E, Shi L, Sun F, Sunagawa S, Sørensen SJ, Thomas A, Tong C, Trajkovski M, Tremblay J, Uritskiy G, Vicedomini R, Wang Z, Wang Z, Wang Z, Warren A, Willassen NP, Yelick K, You R, Zeller G, Zhao Z, Zhu S, Zhu J, Garrido-Oter R, Gastmeier P, Hacquard S, Häußler S, Khaledi A, Maechler F, Mesny F, Radutoiu S, Schulze-Lefert P, Smit N, Strowig T, Bremges A, Sczyrba A, McHardy AC.
Meyer F, et al.
Nat Methods. 2022 Apr;19(4):429-440. doi: 10.1038/s41592-022-01431-4. Epub 2022 Apr 8.
Nat Methods. 2022.
PMID: 35396482
Free PMC article.
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Context-aware genomic surveillance reveals hidden transmission of a carbapenemase-producing Klebsiella pneumoniae.
Viehweger A, Blumenscheit C, Lippmann N, Wyres KL, Brandt C, Hans JB, Hölzer M, Irber L, Gatermann S, Lübbert C, Pletz MW, Holt KE, König B.
Viehweger A, et al.
Microb Genom. 2021 Dec;7(12):000741. doi: 10.1099/mgen.0.000741.
Microb Genom. 2021.
PMID: 34913861
Free PMC article.
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