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scripts
section.3.1.2
section.3.2
section.3.3
section.3.4
seed-kraken @ dd8b930
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README.rst

README.rst

Spaced seeds improve k-mer-based metagenomic classification

This repository contains all supplementary material for paper Spaced seeds improve k-mer-based metagenomic classification by K.Brinda, M.Sykulski, G.Kucherov. Current version available at http://arxiv.org/abs/1502.06256.

Scripts

Snakemake scripts used in Section 3.1.2 (Classifying unaligned reads) and 3.3 (Correlation on real genomes) are available here.

Supplementary plots

Section.3.2

Section.3.3

3 report files with scatter plots of alignment (dis)similarity vs score (hits or coverage), plots in several flavors, experiments on 3 real genomes.

Section.3.4

Plots comparing seed-Kraken with original Kraken, performance and sensitivity on several data sets, spaced seeds of various weights and spans, tables with all results and used seeds.

Seed-Kraken

Seed-Kraken, a modification of Kraken utilizing spaced k-mers instead of contiguous k-mers, is located in a standalone repository. For more details, see its documentation.