Scikit-bio: a fundamental Python library for biological omic data analysis

Matthew Aton; Daniel McDonald; Jorge Cañardo Alastuey; Raeed Azom; Paarth Batra; Valentyn Bezshapkin; Evan Bolyen; Alexander Cagle; J. Gregory Caporaso; Justine W. Debelius; Kestrel Gorlick; Nirmitha Hamsanipally; Lars Hunger; Aryan Keluskar; Disen Liao; Yang Young Lu; Jose A. Navas-Molina; Anders Pitman; Jai Ram Rideout; Anton Sazonov; Bharath Sathappan; Karen Schwarzberg Lipson; Igor Sfiligoi; Chris Tapo; Yoshiki Vázquez-Baeza; Zijun Wu; Zhenjiang Zech Xu; Mingsong Sam Ye; Jianshu Zhao; Rob Knight; James T. Morton; Qiyun Zhu

doi:10.1038/s41592-025-02981-z

Scikit-bio: a fundamental Python library for biological omic data analysis

Matthew Aton
, Daniel McDonald
, Jorge Cañardo Alastuey
, Raeed Azom
, Paarth Batra
, Valentyn Bezshapkin
, Evan Bolyen
, Alexander Cagle
, J. Gregory Caporaso
, Justine W. Debelius
, Kestrel Gorlick
, Nirmitha Hamsanipally
, Lars Hunger
, Aryan Keluskar
, Disen Liao
, Yang Young Lu
, Jose A. Navas-Molina
, Anders Pitman
, Jai Ram Rideout
, Anton Sazonov

Bharath Sathappan, Karen Schwarzberg Lipson, Igor Sfiligoi, Chris Tapo, Yoshiki Vázquez-Baeza, Zijun Wu, Zhenjiang Zech Xu, Mingsong Sam Ye, Jianshu Zhao, Rob Knight, James T. Morton, Qiyun Zhu

Research output: Contribution to journal › Letter › peer-review

7 Scopus citations

Original language	English (US)
Pages (from-to)	274-276
Number of pages	3
Journal	Nature Methods
Volume	23
Issue number	2
DOIs	https://doi.org/10.1038/s41592-025-02981-z
State	Published - Feb 2026
Externally published	Yes

ASJC Scopus subject areas

Biotechnology
Biochemistry
Molecular Biology
Cell Biology

Access to Document

10.1038/s41592-025-02981-z

Cite this

Aton, M., McDonald, D., Cañardo Alastuey, J., Azom, R., Batra, P., Bezshapkin, V., Bolyen, E., Cagle, A., Caporaso, J. G., Debelius, J. W., Gorlick, K., Hamsanipally, N., Hunger, L., Keluskar, A., Liao, D., Lu, Y. Y., Navas-Molina, J. A., Pitman, A., Rideout, J. R., ... Zhu, Q. (2026). Scikit-bio: a fundamental Python library for biological omic data analysis. Nature Methods, 23(2), 274-276. https://doi.org/10.1038/s41592-025-02981-z

Aton, M, McDonald, D, Cañardo Alastuey, J, Azom, R, Batra, P, Bezshapkin, V, Bolyen, E, Cagle, A, Caporaso, JG, Debelius, JW, Gorlick, K, Hamsanipally, N, Hunger, L, Keluskar, A, Liao, D, Lu, YY, Navas-Molina, JA, Pitman, A, Rideout, JR, Sazonov, A, Sathappan, B, Schwarzberg Lipson, K, Sfiligoi, I, Tapo, C, Vázquez-Baeza, Y, Wu, Z, Xu, ZZ, Ye, MS, Zhao, J, Knight, R, Morton, JT & Zhu, Q 2026, 'Scikit-bio: a fundamental Python library for biological omic data analysis', Nature Methods, vol. 23, no. 2, pp. 274-276. https://doi.org/10.1038/s41592-025-02981-z

@article{108c80ed316f409b965bff31aa0785cd,

title = "Scikit-bio: a fundamental Python library for biological omic data analysis",

author = "Matthew Aton and Daniel McDonald and \{Ca{\~n}ardo Alastuey\}, Jorge and Raeed Azom and Paarth Batra and Valentyn Bezshapkin and Evan Bolyen and Alexander Cagle and Caporaso, \{J. Gregory\} and Debelius, \{Justine W.\} and Kestrel Gorlick and Nirmitha Hamsanipally and Lars Hunger and Aryan Keluskar and Disen Liao and Lu, \{Yang Young\} and Navas-Molina, \{Jose A.\} and Anders Pitman and Rideout, \{Jai Ram\} and Anton Sazonov and Bharath Sathappan and \{Schwarzberg Lipson\}, Karen and Igor Sfiligoi and Chris Tapo and Yoshiki V{\'a}zquez-Baeza and Zijun Wu and Xu, \{Zhenjiang Zech\} and Ye, \{Mingsong Sam\} and Jianshu Zhao and Rob Knight and Morton, \{James T.\} and Qiyun Zhu",

year = "2026",

month = feb,

doi = "10.1038/s41592-025-02981-z",

language = "English (US)",

volume = "23",

pages = "274--276",

journal = "Nature Methods",

issn = "1548-7091",

publisher = "Nature Research",

number = "2",

}

TY - JOUR

T1 - Scikit-bio

T2 - a fundamental Python library for biological omic data analysis

AU - Aton, Matthew

AU - McDonald, Daniel

AU - Cañardo Alastuey, Jorge

AU - Azom, Raeed

AU - Batra, Paarth

AU - Bezshapkin, Valentyn

AU - Bolyen, Evan

AU - Cagle, Alexander

AU - Caporaso, J. Gregory

AU - Debelius, Justine W.

AU - Gorlick, Kestrel

AU - Hamsanipally, Nirmitha

AU - Hunger, Lars

AU - Keluskar, Aryan

AU - Liao, Disen

AU - Lu, Yang Young

AU - Navas-Molina, Jose A.

AU - Pitman, Anders

AU - Rideout, Jai Ram

AU - Sazonov, Anton

AU - Sathappan, Bharath

AU - Schwarzberg Lipson, Karen

AU - Sfiligoi, Igor

AU - Tapo, Chris

AU - Vázquez-Baeza, Yoshiki

AU - Wu, Zijun

AU - Xu, Zhenjiang Zech

AU - Ye, Mingsong Sam

AU - Zhao, Jianshu

AU - Knight, Rob

AU - Morton, James T.

AU - Zhu, Qiyun

PY - 2026/2

Y1 - 2026/2

UR - https://www.scopus.com/pages/publications/105024662406

UR - https://www.scopus.com/pages/publications/105024662406#tab=citedBy

U2 - 10.1038/s41592-025-02981-z

DO - 10.1038/s41592-025-02981-z

M3 - Letter

C2 - 41381898

AN - SCOPUS:105024662406

SN - 1548-7091

VL - 23

SP - 274

EP - 276

JO - Nature Methods

JF - Nature Methods

IS - 2

ER -

Scikit-bio: a fundamental Python library for biological omic data analysis

ASJC Scopus subject areas

Access to Document

Other files and links

Cite this