Memory usage of k-mer counting tools when calculating k-mer abundance histograms, with maximum resident program size (y axis, in GB) plotted against the total number of distinct k-mers in the data set (x axis, billions of k-mers).

Benchmarking for elapsed runtime and memory for HAYSTAC, Sigma, Kraken2/Bracken, KrakenUniq and MALT when analysing samples of 10 K, 100 K and 1 M reads against a database of 500 species.

Evangelos A. Dimopoulos (4373215)
Alberto Carmagnini (13889699)
Irina M. Velsko (13889702)
Christina Warinner (513402)
Greger Larson (42564)
Laurent A. F. Frantz (13889705)
Evan K. Irving-Pease (4998092)

September 2022

Memory remains constant as sample size increases, and runtime in most methods (other than Kraken2/Br...

The unappreciated role of k-mers in bioinformatics

Psomopoulos, Fotis

September 2022

This is a talk given in the context of the BSC Life Sessions Abstract k-mers are used on a daily b...

MSPKmerCounter: A Fast and Memory Efficient Approach for K-mer Counting

Yang Li
Xifeng Yan

January 2016

Motivation: A major challenge in next-generation genome seque-ncing (NGS) is to assemble massive ove...

Comparison of the time it takes for k-mer counting tools to calculate k-mer abundance histograms, with time (y axis, in seconds) against data set size (in number of reads, x axis).

Qingpeng Zhang (274356)
Jason Pell (99648)
Rosangela Canino-Koning (604430)
Adina Chuang Howe (604431)
C. Titus Brown (98658)

July 2014

All programs executed in time approximately linear with the number of input reads.</p

Disk storage usage of different k-mer counting tools to calculate k-mer abundance histograms in GB (y axis), plotted against the number of distinct k-mers in the data set (x axis).

Qingpeng Zhang (274356)
Jason Pell (99648)
Rosangela Canino-Koning (604430)
Adina Chuang Howe (604431)
C. Titus Brown (98658)

July 2014

Note that khmer does not use the disk during counting or retrieval, although its hash tables can ...

KMC 2: fast and resource-frugal k-mer counting

Sebastian Deorowicz
Marek Kokot
Szymon Grabowski

January 2015

Motivation: Building the histogram of occurrences of every k-symbol long substring of nucleotide dat...

Time for several k-mer counting tools to retrieve the counts of 9.7 m randomly chosen k-mers (y axis), plotted against the number of distinct k-mers in the data set being queried (x axis).

Qingpeng Zhang (638117)
Jason Pell (99648)
Rosangela Canino-Koning (604430)
Adina Chuang Howe (604431)
C. Titus Brown (98658)

July 2014

BFCounter, DSK, Turtle, KAnalyze, and KMC do not support this functionality.</p

DSK: k-mer counting with very low memory usage

Guillaume Rizk
Dominique Lavenier
Rayan Chikhi

January 2013

Summary: Counting all the k-mers (substrings of length k) in DNA/RNA sequencing reads is the prelimi...

Sequence analysis Advance Access publication January 16, 2013 DSK: k-mer counting with very low memory usage

Guillaume Rizk
Dominique Lavenier
Rayan Chikhi
Michael Brudno

January 2013

Summary: Counting all the k-mers (substrings of length k) in DNA/RNA sequencing reads is the prelimi...

Set-Min Sketch: A Probabilistic Map for Power-Law Distributions with Application to k -Mer Annotation

Shibuya, Yoshihiro
Belazzougui, Djamal
Kucherov, Gregory

February 2022

International audiencek-mer counts are important features used by many bioinformatics pipelines. Exi...

k-mer counting with FPGAs and HMC in-memory operations

Wertenbroek, Rick
Thoma, Yann

April 2019

k-mer counting is an essential algorithm found in many genomic related processes. It may seem like a...

Comparison of memory usages for the six methods.

Xiguo Yuan (110368)
Junying Zhang (28976)
Shengli Zhang (110370)
Guoqiang Yu (110375)
Yue Wang (65477)

December 2012

Memory usage is depicted as a function of genome size when setting the sample size to 50, and is ...

High‐frequency k‐mer counting at low memory footprint

Li Mocheng
Liu Yang
Xiao Nong
Chen Zhiguang

December 2022

Abstract Genomics data analysis requires efficient tools to address the vast amount of data generate...

Comparison of memory usage for different average sequence lengths.

Osvaldo Navarro (578645)
René Cumplido (4789317)
Luis Villaseñor-Pineda (578646)
Claudia Feregrino-Uribe (418810)
Jesús Ariel Carrasco-Ochoa (578647)

June 2014

The figure shows the memory usage of the tested algorithms when processing databases with an aver...

Comparison of memory usage for different number of sequences.

Osvaldo Navarro (578645)
René Cumplido (4789317)
Luis Villaseñor-Pineda (578646)
Claudia Feregrino-Uribe (418810)
Jesús Ariel Carrasco-Ochoa (578647)

June 2014

The figure shows the memory usage obtained when processing databases with a number of sequences v...

Benchmarking for elapsed runtime and memory for HAYSTAC, Sigma, Kraken2/Bracken, KrakenUniq and MALT when analysing samples of 10 K, 100 K and 1 M reads against a database of 500 species.

Evangelos A. Dimopoulos (4373215)
Alberto Carmagnini (13889699)
Irina M. Velsko (13889702)
Christina Warinner (513402)
Greger Larson (42564)
Laurent A. F. Frantz (13889705)
Evan K. Irving-Pease (4998092)

September 2022

Memory remains constant as sample size increases, and runtime in most methods (other than Kraken2/Br...

The unappreciated role of k-mers in bioinformatics

Psomopoulos, Fotis

September 2022

This is a talk given in the context of the BSC Life Sessions Abstract k-mers are used on a daily b...

MSPKmerCounter: A Fast and Memory Efficient Approach for K-mer Counting

Yang Li
Xifeng Yan

January 2016

Motivation: A major challenge in next-generation genome seque-ncing (NGS) is to assemble massive ove...

Comparison of the time it takes for k-mer counting tools to calculate k-mer abundance histograms, with time (y axis, in seconds) against data set size (in number of reads, x axis).

Qingpeng Zhang (274356)
Jason Pell (99648)
Rosangela Canino-Koning (604430)
Adina Chuang Howe (604431)
C. Titus Brown (98658)

July 2014

All programs executed in time approximately linear with the number of input reads.</p

Disk storage usage of different k-mer counting tools to calculate k-mer abundance histograms in GB (y axis), plotted against the number of distinct k-mers in the data set (x axis).

Qingpeng Zhang (274356)
Jason Pell (99648)
Rosangela Canino-Koning (604430)
Adina Chuang Howe (604431)
C. Titus Brown (98658)

July 2014

Note that khmer does not use the disk during counting or retrieval, although its hash tables can ...

KMC 2: fast and resource-frugal k-mer counting

Sebastian Deorowicz
Marek Kokot
Szymon Grabowski

January 2015

Motivation: Building the histogram of occurrences of every k-symbol long substring of nucleotide dat...

Time for several k-mer counting tools to retrieve the counts of 9.7 m randomly chosen k-mers (y axis), plotted against the number of distinct k-mers in the data set being queried (x axis).

Qingpeng Zhang (638117)
Jason Pell (99648)
Rosangela Canino-Koning (604430)
Adina Chuang Howe (604431)
C. Titus Brown (98658)

July 2014

BFCounter, DSK, Turtle, KAnalyze, and KMC do not support this functionality.</p

DSK: k-mer counting with very low memory usage

Guillaume Rizk
Dominique Lavenier
Rayan Chikhi

January 2013

Summary: Counting all the k-mers (substrings of length k) in DNA/RNA sequencing reads is the prelimi...

Sequence analysis Advance Access publication January 16, 2013 DSK: k-mer counting with very low memory usage

Guillaume Rizk
Dominique Lavenier
Rayan Chikhi
Michael Brudno

January 2013

Summary: Counting all the k-mers (substrings of length k) in DNA/RNA sequencing reads is the prelimi...

Set-Min Sketch: A Probabilistic Map for Power-Law Distributions with Application to k -Mer Annotation

Shibuya, Yoshihiro
Belazzougui, Djamal
Kucherov, Gregory

February 2022

International audiencek-mer counts are important features used by many bioinformatics pipelines. Exi...

k-mer counting with FPGAs and HMC in-memory operations

Wertenbroek, Rick
Thoma, Yann

April 2019

k-mer counting is an essential algorithm found in many genomic related processes. It may seem like a...

Comparison of memory usages for the six methods.

Xiguo Yuan (110368)
Junying Zhang (28976)
Shengli Zhang (110370)
Guoqiang Yu (110375)
Yue Wang (65477)

December 2012

Memory usage is depicted as a function of genome size when setting the sample size to 50, and is ...

High‐frequency k‐mer counting at low memory footprint

Li Mocheng
Liu Yang
Xiao Nong
Chen Zhiguang

December 2022

Abstract Genomics data analysis requires efficient tools to address the vast amount of data generate...

Comparison of memory usage for different average sequence lengths.

Osvaldo Navarro (578645)
René Cumplido (4789317)
Luis Villaseñor-Pineda (578646)
Claudia Feregrino-Uribe (418810)
Jesús Ariel Carrasco-Ochoa (578647)

June 2014

The figure shows the memory usage of the tested algorithms when processing databases with an aver...

Comparison of memory usage for different number of sequences.

Osvaldo Navarro (578645)
René Cumplido (4789317)
Luis Villaseñor-Pineda (578646)
Claudia Feregrino-Uribe (418810)
Jesús Ariel Carrasco-Ochoa (578647)

June 2014

The figure shows the memory usage obtained when processing databases with a number of sequences v...

Benchmarking for elapsed runtime and memory for HAYSTAC, Sigma, Kraken2/Bracken, KrakenUniq and MALT when analysing samples of 10 K, 100 K and 1 M reads against a database of 500 species.

Evangelos A. Dimopoulos (4373215)
Alberto Carmagnini (13889699)
Irina M. Velsko (13889702)
Christina Warinner (513402)
Greger Larson (42564)
Laurent A. F. Frantz (13889705)
Evan K. Irving-Pease (4998092)

September 2022

Memory remains constant as sample size increases, and runtime in most methods (other than Kraken2/Br...

The unappreciated role of k-mers in bioinformatics

Psomopoulos, Fotis

September 2022

This is a talk given in the context of the BSC Life Sessions Abstract k-mers are used on a daily b...

MSPKmerCounter: A Fast and Memory Efficient Approach for K-mer Counting

Yang Li
Xifeng Yan

January 2016

Motivation: A major challenge in next-generation genome seque-ncing (NGS) is to assemble massive ove...

Memory usage of k-mer counting tools when calculating k-mer abundance histograms, with maximum resident program size (y axis, in GB) plotted against the total number of distinct k-mers in the data set (x axis, billions of k-mers).

Abstract

Extracted data

Memory usage of k-mer counting tools when calculating k-mer abundance histograms, with maximum resident program size (y axis, in GB) plotted against the total number of distinct k-mers in the data set (x axis, billions of k-mers).

Abstract

Extracted data

Related items

Related items