Both the weighted and unweighted UniFrac distances have been very successfully employed to assess if two communities differ, but do not give any information about how two communities differ. We take advantage of recent observations that the UniFrac metric is equivalent to the so-called earth mover's distance (also known as...
This short note demonstrates that sparse recovery can be achieved by an l₁-minimization ersatz easily implemented using a conventional nonnegative least squares algorithm. A connection with orthogonal matching pursuit is also highlighted. The preliminary results call for more investigations on the potential of the method and on its relations to...
We give a new approach to coding sequence (CDS) density
estimation in genomic analysis based on the topological pressure, which
we develop from a well known concept in ergodic theory. Topological
pressure measures the ‘weighted information content’ of a finite word,
and incorporates 64 parameters which can be interpreted as...
With the decrease in cost and increase in output of whole-genome shotgun technologies, many metagenomic studies are
utilizing this approach in lieu of the more traditional 16S rRNA amplicon technique. Due to the large number of relatively
short reads output from whole-genome shotgun technologies, there is a need for fast...
Full Text:
WGSQuikr: Fast Whole-Genome Shotgun Metagenomic Classification
Koslicki D, Foucart S, Rosen G (2014
With the decrease in cost and increase in output of whole-genome shotgun technologies, many metagenomic studies are
utilizing this approach in lieu of the more traditional 16S rRNA amplicon technique. Due to the large number of relatively
short reads output from whole-genome shotgun technologies, there is a need for fast...
Full Text:
Classification
WGSQuikr: Fast Whole-Genome Shotgun Metagenomic Classification
Koslicki D, Foucart S, Rosen G
With the decrease in cost and increase in output of whole-genome shotgun technologies, many metagenomic studies are utilizing this approach in lieu of the more traditional 16S rRNA amplicon technique. Due to the large number of relatively short reads output from whole-genome shotgun technologies, there is a need for fast...
Motivation:
Estimation of bacterial community composition from high-throughput sequenced 16S rRNA gene amplicons is a key task in microbial ecology. Since the sequence data from each sample typically consist of a large number of reads and are adversely impacted by different levels of biological and technical noise, accurate analysis of...
MOTIVATION: Estimation of bacterial community composition from
a high-throughput sequenced sample is an important task in
metagenomics applications. Since the sample sequence data
typically harbors reads of variable lengths and different levels of
biological and technical noise, accurate statistical analysis of such
data is challenging. Currently popular estimation methods are...