K-mer countingKristian Hovde LilandLars Snipen
By making use of cheap disk space and exploiting CPU and I/O parallelism we propose a very competitivek-mer counting procedure, called KMC. Our results suggest that judicious resource management may allow to solve at least some bioinformatics problems with massive data on a commodity personal comp...
kmer is an R package for rapidly computing distance matrices and clustering large sequence datasets using fast alignment-free k-mer counting and recursive k-means partitioning. Installation To download kmer from CRAN and load the package, run install.packages("kmer") library("kmer") To download ...
kcst - k-mer counting sequence typer Copyright (C) 2018 Marco van Zwetselaario@zwets.it This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License...
Key words: k-mer; k-mer counting; frequency statistic; backward traverse; biological sequence processing 生物序列主要指RNA,DNA及蛋白质序列等. 自人 类基因组计划实施以来, 特别是随着第二代测序技术 大规模的使用与推广, 现今一次深度测序技术可以产 生TB 级的序列数据. 而在对这些海量数据的分析和应 ...
Counting k-mers of sinks in sources amounts to performing the following matrix vector operation: w=m(s)⊺⋅Ms⋅H (2) In order to produce proportions instead of raw counts, we estimate the percentage based on the total number of balls counted per bin (of all known sources). Such ...
为了节省资源,我们可以使用 Jellyfish 这个现成的软件来分析。 JELLYFISH - Fast, Parallel k-mer Counting for DNA Jellyfish mer counter(原来和MaSuRCA是一个开发单位,我说怎么这么眼熟呢)
methods based on countingK-mers by sliding windows are the most interesting classification approach with respect to both speed and accuracy. Here, we present a systematic comparison on five different K-mer based classification methods for the 16S rRNA gene. The methods differ from each other both...
We propose a fast algorithm for calculating Gapped k-mer Kernel using Counting (GaKCo). GaKCo uses associative arrays to calculate the co-occurrence of substrings using cumulative counting. This algorithm is fast, scalable to larger Σ and M, and naturally parallelizable. We provide a rigorous ...
The corrected reads were subjected to 25-nt k-mer counting, resulting in approximately 749.7 and 738.7 millions of non-redundant k-mers for B73 and Mo17, respectively. The similar shapes of the distributions of k-mer abundances (Fig. 1a) and the curves of cumulative contribution of k-...