A fast, lock-free approach for efficient parallel counting of occurrences of k-mers
Guillaume Marçais,Carl Kingsford +1 more
TL;DR: This work proposes a new k-mer counting algorithm and associated implementation, called Jellyfish, which is fast and memory efficient, based on a multithreaded, lock-free hash table optimized for counting k-mers up to 31 bases in length.
read more
Abstract: Motivation: Counting the number of occurrences of every k-mer (substring of length k) in a long string is a central subproblem in many applications, including genome assembly, error correction of sequencing reads, fast multiple sequence alignment and repeat detection. Recently, the deep sequence coverage generated by next-generation sequencing technologies has caused the amount of sequence to be processed during a genome project to grow rapidly, and has rendered current k-mer counting tools too slow and memory intensive. At the same time, large multicore computers have become commonplace in research facilities allowing for a new parallel computational paradigm.
Results: We propose a new k-mer counting algorithm and associated implementation, called Jellyfish, which is fast and memory efficient. It is based on a multithreaded, lock-free hash table optimized for counting k-mers up to 31 bases in length. Due to their flexibility, suffix arrays have been the data structure of choice for solving many string problems. For the task of k-mer counting, important in many biological applications, Jellyfish offers a much faster and more memory-efficient solution.
Availability: The Jellyfish software is written in C++ and is GPL licensed. It is available for download at http://www.cbcb.umd.edu/software/jellyfish.
Contact: [email protected]
Supplementary information:Supplementary data are available at Bioinformatics online.
read more
Chat with Paper
AI Agents for this Paper
Find similar papers on Google Scholar, PubMed and Arxiv
Write a critical review of this paper
Analyze citations of this paper to find unaddressed research gaps
Citations
Chromosome-level genome assembly of a cyprinid fish Onychostoma macrolepis by integration of nanopore sequencing, Bionano and Hi-C technology.
Lina Sun,Tian Gao,Feilong Wang,Zuliang Qin,Longxia Yan,Wenjing Tao,Minghui Li,Canbiao Jin,Li Ma,Thomas D. Kocher,Deshou Wang +10 more
TL;DR: The chromosome‐level assembly of the O.macrolepis genome obtained from the integration of nanopore long‐read sequencing with physical maps produced using Bionano and Hi‐C technology provides a valuable genomic resource for further biological and evolutionary studies of O. macrolepis.
33
De novo genome assembly and in natura epigenomics reveal salinity-induced DNA methylation in the mangrove tree Bruguiera gymnorhiza.
TL;DR: In this paper, the authors performed a de novo genome assembly and in natura epigenome analyses of the mangrove Bruguiera gymnorhiza, one of the dominant species in the world.
33
The absence of the caffeine synthase gene is involved in the naturally decaffeinated status of Coffea humblotiana, a wild species from Comoro archipelago.
Nathalie Raharimalala,Stephane Rombauts,Andrew McCarthy,Andrea Garavito,Simon Orozco-Arias,Laurence Bellanger,Alexa Yadira Morales-Correa,Solène Froger,Stéphane Michaux,Victoria Berry,Sylviane Metairon,Coralie Fournier,Coralie Fournier,Maud Lepelley,Lukas A. Mueller,Emmanuel Couturon,Perla Hamon,Jean Jacques Rakotomalala,Patrick Descombes,Romain Guyot,Dominique Crouzillat +20 more
TL;DR: In this article, the authors reported on the 422-Mb chromosome-level assembly of the Coffea humblotiana genome, a wild and endangered, naturally caffeine-free species from the Comoro archipelago.
The bHLH-zip transcription factor SREBP regulates triterpenoid and lipid metabolisms in the medicinal fungus Ganoderma lingzhi
Yong-Nan Liu,Feng-Yuan Wu,Renyuan Tian,Ziqin Xu,Ji-Ye Liu,Jia Huang,Fei-Fei Xue,Biyun Liu,Gao-Qiang Liu +8 more
TL;DR: In this paper , the authors identify putative targets of the transcription factor sterol regulatory element-binding protein (SREBP), including the genes of triterpenoid synthesis and lipid metabolism.
The evolutionary history and diagnostic utility of the CRISPR-Cas system within Salmonella enterica ssp. enterica
James B. Pettengill,Ruth Timme,Rodolphe Barrangou,Magaly Toro,Marc W. Allard,Errol Strain,Steven M. Musser,Eric W. Brown +7 more
TL;DR: A novel clustering approach based onCRISPR spacer content is developed, but it is found that typing based on CRISPRs was less accurate than the MLST-based alternative; typed based on WGS data was the most accurate.
33
References
MUSCLE: multiple sequence alignment with high accuracy and high throughput
TL;DR: MUSCLE is a new computer program for creating multiple alignments of protein sequences that includes fast distance estimation using kmer counting, progressive alignment using a new profile function the authors call the log-expectation score, and refinement using tree-dependent restricted partitioning.
45.1K
•Book
Introduction to Algorithms
Thomas H. Cormen,Charles E. Leiserson,Ronald L. Rivest +2 more
- 01 Jan 1990
TL;DR: The updated new edition of the classic Introduction to Algorithms is intended primarily for use in undergraduate or graduate courses in algorithms or data structures and presents a rich variety of algorithms and covers them in considerable depth while making their design and analysis accessible to all levels of readers.
24.8K
MapReduce: simplified data processing on large clusters
Jeffrey Dean,Sanjay Ghemawat +1 more
- 06 Dec 2004
TL;DR: This paper presents the implementation of MapReduce, a programming model and an associated implementation for processing and generating large data sets that runs on a large cluster of commodity machines and is highly scalable.
MapReduce: simplified data processing on large clusters
Jeffrey Dean,Sanjay Ghemawat +1 more
TL;DR: This presentation explains how the underlying runtime system automatically parallelizes the computation across large-scale clusters of machines, handles machine failures, and schedules inter-machine communication to make efficient use of the network and disks.
A Whole-Genome Assembly of Drosophila
Eugene W. Myers,Granger G. Sutton,Arthur L. Delcher,Ian M. Dew,Dan P. Fasulo,Michael Flanigan,Saul A. Kravitz,Clark M. Mobarry,Knut Reinert,Karin A. Remington,Eric L. Anson,Randall Bolanos,Hui-Hsien Chou,Catherine Jordan,Aaron L. Halpern,Stefano Lonardi,Ellen M. Beasley,Rhonda C. Brandon,Lin Chen,Patrick J. Dunn,Zhongwu Lai,Yong Liang,Deborah R. Nusskern,Ming Zhan,Qing Zhang,Xiangqun Zheng,Gerald M. Rubin,Mark Raymond Adams,J. Craig Venter +28 more
TL;DR: The quality of a whole-genome assembly of Drosophila melanogaster and the nature of the computer algorithms that accomplished it are reported on and should be of substantial value to the scientific community.
1.6K