Tag: experiments

RADinitio 1.1.1 – Simulation software for the Selection and Optimization of RADseq Experiments

RADinitio 1.1.1

:: DESCRIPTION

RADinitio is a forward simulator for creating population-level RAD data sets, based on a given reference genome. This in silico RADseq library preparation and sequencing process, allows for the exploration of parameters including restriction enzyme selection, library insert size, PCR duplicate distribution, and sequencing coverage.

DEVELOPER

Cresko labs

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

RADinitio

:: MORE INFORMATION

Citation:

Rivera-Colón AG, Rochette NC, Catchen JM.
Simulation with RADinitio improves RADseq experimental design and sheds light on sources of missing data.
Mol Ecol Resour. 2021 Feb;21(2):363-378. doi: 10.1111/1755-0998.13163. Epub 2020 May 20. PMID: 32275349.

BSeQC 1.4 – Quality Control of Bisulfite Sequencing Experiments

BSeQC 1.4

:: DESCRIPTION

BSeQC is a quality control package specially for bisulfite sequencing experiments. It can comprehensively evaluate the quality of BS-seq experiments and automatically trim nucleotides with potential technical biases. In addition, BSeQC also support removing duplicate reads and keeping one copy of the overlapping segment in paired-end sequencing.

::DEVELOPER

Li Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 BSeQC

:: MORE INFORMATION

Citation

Bioinformatics, 29 (24), 3227-9 2013 Dec 15
BSeQC: Quality Control of Bisulfite Sequencing Experiments
Xueqiu Lin , Deqiang Sun, Benjamin Rodriguez, Qian Zhao, Hanfei Sun, Yong Zhang, Wei Li

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