The khmer software package: Enabling efficient nucleotide sequence analysis

C. Titus Brown; Michael R. Crusoe; Hussien F. Alameldin; Sherine Awad; Elmar Boucher; Adam Caldwell; Reed Cartwright; Amanda Charbonneau; Bede Constantinides; Greg Edvenson; Scott Fay; Jacob Fenton; Thomas Fenzl; Jordan Fish; Leonor Garcia-Gutierrez; Phillip Garland; Jonathan Gluck; Iván González; Sarah Guermond; Jiarong Guo; Aditi Gupta; Joshua R. Herr; Adina Howe; Alex Hyer; Andreas Härpfer; Luiz Irber; Rhys Kidd; David Lin; Justin Lippi; Tamer Mansour; Pamela McA'Nulty; Eric McDonald; Jessica Mizzi; Kevin D. Murray; Joshua R. Nahum; Kaben Nanlohy; Alexander Johan Nederbragt; Humberto Ortiz-Zuazaga; Jeramia Ory; Jason Pell; Charles Pepe-Ranney; Zachary N. Russ; Erich Schwarz; Camille Scott; Josiah Seaman; Scott Sievert; Jared Simpson; Connor T. Skennerton; James Spencer; Ramakrishnan Srinivasan; Daniel Standage; James A. Stapleton; Susan R. Steinman; Joe Stein; Benjamin Taylor; Will Trimble; Heather L. Wiencko; Michael Wright; Brian Wyss; Qingpeng Zhang; En Zyme

doi:10.12688/f1000research.6924.1

The khmer software package: Enabling efficient nucleotide sequence analysis

C. Titus Brown, Michael R. Crusoe, Hussien F. Alameldin, Sherine Awad, Elmar Boucher, Adam Caldwell, Reed Cartwright, Amanda Charbonneau, Bede Constantinides, Greg Edvenson, Scott Fay, Jacob Fenton, Thomas Fenzl, Jordan Fish, Leonor Garcia-Gutierrez, Phillip Garland, Jonathan Gluck, Iván González, Sarah Guermond, Jiarong GuoAditi Gupta, Joshua R. Herr, Adina Howe, Alex Hyer, Andreas Härpfer, Luiz Irber, Rhys Kidd, David Lin, Justin Lippi, Tamer Mansour, Pamela McA'Nulty, Eric McDonald, Jessica Mizzi, Kevin D. Murray, Joshua R. Nahum, Kaben Nanlohy, Alexander Johan Nederbragt, Humberto Ortiz-Zuazaga, Jeramia Ory, Jason Pell, Charles Pepe-Ranney, Zachary N. Russ, Erich Schwarz, Camille Scott, Josiah Seaman, Scott Sievert, Jared Simpson, Connor T. Skennerton, James Spencer, Ramakrishnan Srinivasan, Daniel Standage, James A. Stapleton, Susan R. Steinman, Joe Stein, Benjamin Taylor, Will Trimble, Heather L. Wiencko, Michael Wright, Brian Wyss, Qingpeng Zhang, En Zyme

CLAS-NS: Life Sciences, School of (SOLS)

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

156 Scopus citations

Abstract

The khmer package is a freely available software library for working efficiently with fixed length DNA words, or k-mers. khmer provides implementations of a probabilistic k-mer counting data structure, a compressible De Bruijn graph representation, De Bruijn graph partitioning, and digital normalization. khmer is implemented in C++ and Python, and is freely available under the BSD license at https://github.com/dib-lab/khmer/.

Original language	English (US)
Article number	900
Journal	F1000Research
Volume	4
DOIs	https://doi.org/10.12688/f1000research.6924.1
State	Published - 2015

Keywords

Bioinformatics
Dna sequencing analysis
K-mer
Khmer
Kmer
Low-memory
Online
Streaming

ASJC Scopus subject areas

Biochemistry, Genetics and Molecular Biology(all)
Immunology and Microbiology(all)
Pharmacology, Toxicology and Pharmaceutics(all)

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Brown, C. T., Crusoe, M. R., Alameldin, H. F., 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., ... Zyme, E. (2015). The khmer software package: Enabling efficient nucleotide sequence analysis. F1000Research, 4, [900]. https://doi.org/10.12688/f1000research.6924.1

The khmer software package : Enabling efficient nucleotide sequence analysis. / Brown, C. Titus; Crusoe, Michael R.; Alameldin, Hussien F.; Awad, Sherine; Boucher, Elmar; Caldwell, Adam; Cartwright, Reed; Charbonneau, Amanda; Constantinides, Bede; Edvenson, Greg; Fay, Scott; Fenton, Jacob; Fenzl, Thomas; Fish, Jordan; Garcia-Gutierrez, Leonor; Garland, Phillip; Gluck, Jonathan; González, Iván; Guermond, Sarah; Guo, Jiarong; Gupta, Aditi; Herr, Joshua R.; Howe, Adina; Hyer, Alex; Härpfer, Andreas; Irber, Luiz; Kidd, Rhys; Lin, David; Lippi, Justin; Mansour, Tamer; McA'Nulty, Pamela; McDonald, Eric; Mizzi, Jessica; Murray, Kevin D.; Nahum, Joshua R.; Nanlohy, Kaben; Nederbragt, Alexander Johan; Ortiz-Zuazaga, Humberto; Ory, Jeramia; Pell, Jason; Pepe-Ranney, Charles; Russ, Zachary N.; Schwarz, Erich; Scott, Camille; Seaman, Josiah; Sievert, Scott; Simpson, Jared; Skennerton, Connor T.; Spencer, James; Srinivasan, Ramakrishnan; Standage, Daniel; Stapleton, James A.; Steinman, Susan R.; Stein, Joe; Taylor, Benjamin; Trimble, Will; Wiencko, Heather L.; Wright, Michael; Wyss, Brian; Zhang, Qingpeng; Zyme, En.

In: F1000Research, Vol. 4, 900, 2015.

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

Brown, CT, 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 2015, 'The khmer software package: Enabling efficient nucleotide sequence analysis', F1000Research, vol. 4, 900. https://doi.org/10.12688/f1000research.6924.1

Brown, C. Titus ; Crusoe, Michael R. ; Alameldin, Hussien F. ; Awad, Sherine ; Boucher, Elmar ; Caldwell, Adam ; Cartwright, Reed ; Charbonneau, Amanda ; Constantinides, Bede ; Edvenson, Greg ; Fay, Scott ; Fenton, Jacob ; Fenzl, Thomas ; Fish, Jordan ; Garcia-Gutierrez, Leonor ; Garland, Phillip ; Gluck, Jonathan ; González, Iván ; Guermond, Sarah ; Guo, Jiarong ; Gupta, Aditi ; Herr, Joshua R. ; Howe, Adina ; Hyer, Alex ; Härpfer, Andreas ; Irber, Luiz ; Kidd, Rhys ; Lin, David ; Lippi, Justin ; Mansour, Tamer ; McA'Nulty, Pamela ; McDonald, Eric ; Mizzi, Jessica ; Murray, Kevin D. ; Nahum, Joshua R. ; Nanlohy, Kaben ; Nederbragt, Alexander Johan ; Ortiz-Zuazaga, Humberto ; Ory, Jeramia ; Pell, Jason ; Pepe-Ranney, Charles ; Russ, Zachary N. ; Schwarz, Erich ; Scott, Camille ; Seaman, Josiah ; Sievert, Scott ; Simpson, Jared ; Skennerton, Connor T. ; Spencer, James ; Srinivasan, Ramakrishnan ; Standage, Daniel ; Stapleton, James A. ; Steinman, Susan R. ; Stein, Joe ; Taylor, Benjamin ; Trimble, Will ; Wiencko, Heather L. ; Wright, Michael ; Wyss, Brian ; Zhang, Qingpeng ; Zyme, En. / The khmer software package : Enabling efficient nucleotide sequence analysis. In: F1000Research. 2015 ; Vol. 4.

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title = "The khmer software package: Enabling efficient nucleotide sequence analysis",

abstract = "The khmer package is a freely available software library for working efficiently with fixed length DNA words, or k-mers. khmer provides implementations of a probabilistic k-mer counting data structure, a compressible De Bruijn graph representation, De Bruijn graph partitioning, and digital normalization. khmer is implemented in C++ and Python, and is freely available under the BSD license at https://github.com/dib-lab/khmer/.",

keywords = "Bioinformatics, Dna sequencing analysis, K-mer, Khmer, Kmer, Low-memory, Online, Streaming",

author = "Brown, {C. Titus} and Crusoe, {Michael R.} and Alameldin, {Hussien F.} and Sherine Awad and Elmar Boucher and Adam Caldwell and Reed Cartwright and Amanda Charbonneau and Bede Constantinides and Greg Edvenson and Scott Fay and Jacob Fenton and Thomas Fenzl and Jordan Fish and Leonor Garcia-Gutierrez and Phillip Garland and Jonathan Gluck and Iv{\'a}n Gonz{\'a}lez and Sarah Guermond and Jiarong Guo and Aditi Gupta and Herr, {Joshua R.} and Adina Howe and Alex Hyer and Andreas H{\"a}rpfer and Luiz Irber and Rhys Kidd and David Lin and Justin Lippi and Tamer Mansour and Pamela McA'Nulty and Eric McDonald and Jessica Mizzi and Murray, {Kevin D.} and Nahum, {Joshua R.} and Kaben Nanlohy and Nederbragt, {Alexander Johan} and Humberto Ortiz-Zuazaga and Jeramia Ory and Jason Pell and Charles Pepe-Ranney and Russ, {Zachary N.} and Erich Schwarz and Camille Scott and Josiah Seaman and Scott Sievert and Jared Simpson and Skennerton, {Connor T.} and James Spencer and Ramakrishnan Srinivasan and Daniel Standage and Stapleton, {James A.} and Steinman, {Susan R.} and Joe Stein and Benjamin Taylor and Will Trimble and Wiencko, {Heather L.} and Michael Wright and Brian Wyss and Qingpeng Zhang and En Zyme",

note = "Funding Information: is now funded by the ?ational Human Genome Research Institute of the ?ational Institutes of Health under Award ?umber R01HG007513, as well as by the the Gordon and Betty Moore Foundation under Award number GBMF4551, all to CTB. Funding Information: Grant information: khmer development has largely been supported by AFRI Competitive Grant no. 2010-65205-20361 from the USDA ?IFA, and Publisher Copyright: {\textcopyright} 2015 Crusoe MR et al.",

year = "2015",

doi = "10.12688/f1000research.6924.1",

language = "English (US)",

volume = "4",

journal = "F1000Research",

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AU - Brown, C. Titus

AU - Crusoe, Michael R.

AU - Alameldin, Hussien F.

AU - Awad, Sherine

AU - Boucher, Elmar

AU - Caldwell, Adam

AU - Cartwright, Reed

AU - Charbonneau, Amanda

AU - Constantinides, Bede

AU - Edvenson, Greg

AU - Fay, Scott

AU - Fenton, Jacob

AU - Fenzl, Thomas

AU - Fish, Jordan

AU - Garcia-Gutierrez, Leonor

AU - Garland, Phillip

AU - Gluck, Jonathan

AU - González, Iván

AU - Guermond, Sarah

AU - Guo, Jiarong

AU - Gupta, Aditi

AU - Herr, Joshua R.

AU - Howe, Adina

AU - Hyer, Alex

AU - Härpfer, Andreas

AU - Irber, Luiz

AU - Kidd, Rhys

AU - Lin, David

AU - Lippi, Justin

AU - Mansour, Tamer

AU - McA'Nulty, Pamela

AU - McDonald, Eric

AU - Mizzi, Jessica

AU - Murray, Kevin D.

AU - Nahum, Joshua R.

AU - Nanlohy, Kaben

AU - Nederbragt, Alexander Johan

AU - Ortiz-Zuazaga, Humberto

AU - Ory, Jeramia

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AU - Seaman, Josiah

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AU - Simpson, Jared

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AU - Spencer, James

AU - Srinivasan, Ramakrishnan

AU - Standage, Daniel

AU - Stapleton, James A.

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AU - Stein, Joe

AU - Taylor, Benjamin

AU - Trimble, Will

AU - Wiencko, Heather L.

AU - Wright, Michael

AU - Wyss, Brian

AU - Zhang, Qingpeng

AU - Zyme, En

N1 - Funding Information: is now funded by the ?ational Human Genome Research Institute of the ?ational Institutes of Health under Award ?umber R01HG007513, as well as by the the Gordon and Betty Moore Foundation under Award number GBMF4551, all to CTB. Funding Information: Grant information: khmer development has largely been supported by AFRI Competitive Grant no. 2010-65205-20361 from the USDA ?IFA, and Publisher Copyright: © 2015 Crusoe MR et al.

PY - 2015

Y1 - 2015

N2 - The khmer package is a freely available software library for working efficiently with fixed length DNA words, or k-mers. khmer provides implementations of a probabilistic k-mer counting data structure, a compressible De Bruijn graph representation, De Bruijn graph partitioning, and digital normalization. khmer is implemented in C++ and Python, and is freely available under the BSD license at https://github.com/dib-lab/khmer/.

AB - The khmer package is a freely available software library for working efficiently with fixed length DNA words, or k-mers. khmer provides implementations of a probabilistic k-mer counting data structure, a compressible De Bruijn graph representation, De Bruijn graph partitioning, and digital normalization. khmer is implemented in C++ and Python, and is freely available under the BSD license at https://github.com/dib-lab/khmer/.

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KW - Dna sequencing analysis

KW - K-mer

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KW - Kmer

KW - Low-memory

KW - Online

KW - Streaming

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JO - F1000Research

JF - F1000Research

SN - 2046-1402

M1 - 900

ER -

The khmer software package: Enabling efficient nucleotide sequence analysis

Abstract

Keywords

ASJC Scopus subject areas

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