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The khmer software package: enabling efficient nucleotide sequence analysis version 1; peer review: 2 approved, 1 approved with reservations

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

in Bioinformatics / Software Tool

2015

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The khmer software package: enabling efficient nucleotide sequence analysis version 1; peer review: 2 approved, 1 approved with reservations

in Bioinformatics / Software Tool

2015

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The khmer software package: enabling efficient nucleotide sequence analysis version 1; peer review: 2 approved, 1 approved with reservations

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2015

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Journal Article

The khmer software package: enabling efficient nucleotide sequence analysis version 1; peer review: 2 approved, 1 approved with reservations

Charbonneau, Amanda,

Guermond, Sarah,

Hyer, Alex,

Murray, Kevin D,

Härpfer, Andreas,

Wyss, Brian,

Standage, Daniel,

Awad, Sherine,

Crusoe, Michael R,

Fish, Jordan,

Ory, Jeramia,

Gluck, Jonathan,

Fenton, Jacob,

Edvenson, Greg,

Kidd, Rhys,

Gupta, Aditi,

Nanlohy, Kaben,

Garcia-Gutierrez, Leonor,

Howe, Adina,

Fenzl, Thomas,

Zhang, Qingpeng,

Nederbragt, Alexander Johan,

Brown, C. Titus,

González, Iván,

Seaman, Josiah,

Schwarz, Erich,

Wright, Michael,

Lippi, Justin,

Wiencko, Heather L,

McA'Nulty, Pamela,

Herr, Joshua R,

Irber, Luiz,

Srinivasan, Ramakrishnan,

Ortiz-Zuazaga, Humberto,

Trimble, Will,

Nahum, Joshua R,

Pell, Jason,

Constantinides, Bede,

Fay, Scott,

Pepe-Ranney, Charles,

Caldwell, Adam,

Scott, Camille,

Simpson, Jared,

Skennerton, Connor T,

Alameldin, Hussien F,

Sievert, Scott,

Stein, Joe,

Taylor, Benjamin,

Russ, Zachary N,

Stapleton, James A,

Mansour, Tamer,

Boucher, Elmar,

zyme, en,

Guo, Jiarong,

Garland, Phillip,

Lin, David,

Spencer, James,

Cartwright, Reed,

McDonald, Eric,

Mizzi, Jessica,

Steinman, Susan R

2015

Overview

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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Publisher

F1000Research,F1000 Research Ltd

Subject

Bioinformatics

/ Software Tool