Rainbow: an integrated tool for efficient clustering and assembling RAD-seq reads
Rainbow is developed to provide an ultra-fast and memory-efficient solution to clustering and assembling short reads p...w not only outputs the optimal but also suboptimal assembly results. Based on simulati...2036 days ago
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sim3C: Read-pair simulation of 3C-based sequencing methodologies (HiC, Meta3C, DNase-HiC)
Required python modules biopython intervaltree numpy scipy tqdm PyYAML2011 days ago
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ChIPulate: A Python3 framework to simulate read counts in a ChIP-seq experiment
ChIP-seq simulation pipeline, ChIPulate, we assess the impact of various biological and experimental sources of variation on several outcomes of a ChIP-seq experiment, v...1879 days ago
OMTools: a software package for visualizing and processing optical mapping data
OMTools, an efficient and intuitive data processing and visualization suite to handle and explore large-scale optical...les. OMTools includes modules for visualization (OMView), data processing and simulati...1875 days ago
Patterns: a modeling tool dedicated to biological network modeling
It is designed to work with patterned data. Famous examples of problems related to patterned data are: recovering signals in networks after a stimulation (cascade network reverse engineering), analysing periodic signals.1756 days ago
ALF--a simulation framework for genome evolution.
Artificial Life Framework (ALF) simulates a root genome into a number of related genomes. Result files include the res...iel A Dalquen, Maria Anisimova, Gaston H Gonnet, Christophe Dessimoz: ALF - A Simulati...1667 days ago
simuG: a general-purpose genome simulator
Simulated genomes with pre-defined and random genomic variants can be very useful for benchmarking genomic and bioinfo...f simuG make it a unique general-purpose genome simulator for a wide-range of simulati...1631 days ago