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nick_youngblut - Department of Microbiome Science
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nick_youngblut

Department of Microbiome Science
Max Planck Society • Munich • Germany

http://www.leylab.com/people/

http://www.eb.tuebingen.mpg.de/nc/research/departments/microbiome-science/staff-microbiome-science.html

Skills and expertise

Fields of interest
  • WGS analysis
  • Metagenomic sequencing analysis
  • aCGH data analysis
Languages
  • English
Programming languages
  • Python
  • R

Reviews and Discussions

LATEST REVIEWS

PhyloPhlAn 2017-11-01, 09:32:49
It is not available via conda. It requires usearch (and vsearch cannot just be substituted). Also, it requires running the phylophlan.py within the same directory *and* all of your files MUST be in…
ITEP 2016-12-05, 08:27:08
ITEP has pretty good documentation and support. Setup is pretty straight-forward, but it's not integrated into conda or other package managers. ITEP is great for creating a database that can be…

LATEST DISCUSSIONS

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TOOLS MAINTAINED

HTSSIP

Desktop

HTSSIP

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Consists of a standardized analysis software. HTSSIP simplifies reproducible analyses on high throughput sequencing with stable isotope probing (HTS-SIP) datasets and direct cross-study comparisons.…

SIPSim

Desktop

SIPSim

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Models stable isotope probing of nucleic acids (DNA-SIP) data and assesses how changes in key SIP experimental parameters are predicted to affect DNA-SIP accuracy. SIPSim can feign the distribution…

Fields of interest

WGS analysis
Sifts true de novo mutations (DNMs) from noise. HAPDeNovo drastically…
Assists users in optimized block trimming. This algorithm is a polynomial-time…
Encodes string sequence into a mathematical representation. Nucl2Vec aims to…
Metagenomic sequencing analysis
Studies dated genetic data allowing the determination of evolutionary rates and…
Assists users in optimized block trimming. This algorithm is a polynomial-time…
Enables users to reconstruct genome-scale metabolic models for any organism…
aCGH data analysis
Enables spatial mapping of RNA-seq transcript data onto high resolution tissue…
Permits user to work on segmentation of genomic and epigenomic profiles. iSeg…
Combines several steps for a high-quality probe and primer design for a variety…