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

Sebastian Deorowicz, Marek Kokot, Szymon Grabowski, Agnieszka Debudaj-Grabysz
2015 Computer applications in the biosciences : CABIOS  
The tremendous amounts of NGS data require fast algorithms for k-mer counting, preferably using moderate amounts of memory.  ...  Results: We present a novel method for k-mer counting, on large datasets at least twice faster than the strongest competitors (Jellyfish 2, KMC 1), using about 12 GB (or less) of RAM memory.  ...  The presented KMC 2 algorithm is currently the fastest k-mer counter, with modest resource (memory and disk) requirements.  ... 
doi:10.1093/bioinformatics/btv022 pmid:25609798 fatcat:nteraui7abdk5bicld3vq2cqda

Disk-based k-mer counting on a PC

Sebastian Deorowicz, Agnieszka Debudaj-Grabysz, Szymon Grabowski
2013 BMC Bioinformatics  
Conclusions: By making use of cheap disk space and exploiting CPU and I/O parallelism we propose a very competitive k-mer counting procedure, called KMC.  ...  Results: We propose a simple, yet efficient, parallel disk-based algorithm for counting k-mers.  ...  Acknowledgements The work was supported by the Polish National Science Center upon decision DEC-2011/01/B/ST6/06868 (first author), and by Silesian University of Technology under the project BK-220/RAu2  ... 
doi:10.1186/1471-2105-14-160 pmid:23679007 pmcid:PMC3680041 fatcat:z5374zj3ufchdolldb6ij3kidu

Scalable, ultra-fast, and low-memory construction of compacted de Bruijn graphs with Cuttlefish 2 [article]

Jamshed Khan, Marek Kokot, Sebastian Deorowicz, Rob Patro
2021 bioRxiv   pre-print
Cuttlefish 2 is implemented in C++14, and is available as open-source software under a BSD-3-Clause license at https://github.com/COMBINE-lab/cuttlefish.  ...  We present Cuttlefish 2, significantly advancing the existing state-of-the-art methods for construction of this graph.  ...  In this paper, we present a fast and memory-frugal algorithm for constructing compacted de Bruijn graphs, CUTTLEFISH 2, applicable both on raw sequencing short-reads and assembled references, that can  ... 
doi:10.1101/2021.12.14.472718 fatcat:z2mqu7kfzvhzne5nacgroe745y

Gerbil: A Fast and Memory-Efficient k-mer Counter with GPU-Support [article]

Marius Erbert, Steffen Rechner, Matthias Müller-Hannemann
2016 arXiv   pre-print
While existing k-mer counting tools suffer from excessive memory resource consumption or degrading performance for large k, Gerbil is able to efficiently support large k without much loss of performance  ...  We present the open source k-mer counting software Gerbil that has been designed for the efficient counting of k-mers for k≥32.  ...  The result is a k-mer counting tool that is both time efficient and memory frugal. 1 In addition, Gerbil can optionally use GPUs to accelerate the counting step.  ... 
arXiv:1607.06618v1 fatcat:3xvtaxvuqrhizfazrhhfcd6ssi

Gerbil: A Fast and Memory-Efficient k-mer Counter with GPU-Support [chapter]

Marius Erbert, Steffen Rechner, Matthias Müller-Hannemann
2016 Lecture Notes in Computer Science  
Existing k-mer counting tools are most often optimized for small k < 32 and suffer from excessive memory resource consumption or degrading performance for large k.  ...  Results: We present the open source k-mer counting software Gerbil that has been designed for the efficient counting of k-mers for k ≥ 32.  ...  The result is a k-mer counting tool that is both time efficient and memory frugal. 1 In addition, Gerbil can optionally use GPUs to accelerate the counting step.  ... 
doi:10.1007/978-3-319-43681-4_12 fatcat:urbeg4rg2rcyzgkjvtqbxchxee

Gerbil: a fast and memory-efficient k-mer counter with GPU-support

Marius Erbert, Steffen Rechner, Matthias Müller-Hannemann
2017 Algorithms for Molecular Biology  
Existing k-mer counting tools are most often optimized for small k < 32 and suffer from excessive memory resource consumption or degrading performance for large k.  ...  Results: We present the open source k-mer counting software Gerbil that has been designed for the efficient counting of k-mers for k ≥ 32.  ...  The result is a k-mer counting tool that is both time efficient and memory frugal. 1 In addition, Gerbil can optionally use GPUs to accelerate the counting step.  ... 
doi:10.1186/s13015-017-0097-9 pmid:28373894 pmcid:PMC5374613 fatcat:gargokf5vvhp5fi537j4wrobxi

Minimizer-space de Bruijn graphs [article]

Barış Ekim, Bonnie Berger, Rayan Chikhi
2021 bioRxiv   pre-print
By projecting DNA sequences into ordered lists of minimizers, our key idea is to enumerate what we call k-min-mers, that are k-mers over a larger alphabet consisting of minimizer tokens.  ...  For assembly, we implemented mdBG in software we call rust-mdbg, resulting in ultra-fast, low memory and highly-contiguous assembly of PacBio HiFi reads.  ...  R.C. was funded by ANR Inception (ANR-16-CONV-0005) and PRAIRIE (ANR-19-P3IA-0001) grants. B.B. and B.E. were funded by the NIH R01HG010959 grant. The authors are grateful to A. Limasset and B.  ... 
doi:10.1101/2021.06.09.447586 fatcat:nd5cpfpoezfl7aixjaumldjzyy

The Role of Distributed Computing in Big Data Science: Case Studies in Forensics and Bioinformatics [article]

Gianluca Roscigno, Universita' Degli Studi Di Salerno, Universita' Degli Studi Di Salerno
2017
However, without any algorithm engineering activity, some target applications are not alto- gether fast and e cient, and they can su er from several problems and drawbacks when are executed on a distributed  ...  Therefore, it is required to assess how distributed solutions are run on a Hadoop cluster, and/or how their performance can be improved to reduce resources consumption and completion times.  ...  input management, fast local k-mers extraction, two-levels k-mers aggregation with explicit partitioning and memory-frugal requirements.  ... 
doi:10.14273/unisa-725 fatcat:e3ysdvu32vhehef2fccltvqrxm

Easton Gazette, and Eastern Shore Intelligencer 06-1819

(:Unkn) Unknown
1819
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doi:10.13016/m2qb9v570 fatcat:wadt7r5lwzeyzb3e6if62yz5xm