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KMC 2: fast and resource-frugal k-mer counting
2015
Computer applications in the biosciences : CABIOS
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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
2013
BMC Bioinformatics
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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]
2021
bioRxiv
pre-print
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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]
2016
arXiv
pre-print
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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]
2016
Lecture Notes in Computer Science
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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
2017
Algorithms for Molecular Biology
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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]
2021
bioRxiv
pre-print
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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]
2017
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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
1819
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m prieHd»i jmti fcĥ oc J»l,do rV*k", do <to NngWuv" fcShf*' and ch *d SftWnet, ok Pattino, . ', do Inch c»»pe do. Me ' fe K^BAiat 289: U dear prqfit 'i U per acre B. ...
He fctattd that he had been bitten in his right arm by a large dog on the 20th of February fast, at 2 o'clock, A. M. while discharging his duty as city Watchman. ...
object as soon as possible; and our prbsnects of doing the same speedily are .very. favorable from the ample resources pro-ROBBERY. ...
doi:10.13016/m2qb9v570
fatcat:wadt7r5lwzeyzb3e6if62yz5xm