IDBA-UD is a iterative De Bruijn Graph De Novo Assembler for Short Reads Sequencing data with Highly Uneven Sequencing Depth.
The IDR (Irreproducible Discovery Rate) framework is a uniﬁed approach to measure the reproducibility of ﬁndings identiﬁed from replicate experiments and provide highly stable thresholds based on reproducibility.
An open source and free collection of network analysis tool.
Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations.
command line tools for IGV
a simple, user-friendly tool for interactive image classification, segmentation and analysis
IMa3 can be used to solve a fundamental problem in evolutionary genetics, which is to jointly consider phylogenetic history and pouplation genetic history, including gene exchange. IMa3 can be used to estimate the rooted phylogenetic tree for multiple populations, and does so while integrating over all possible Isolation-with-Migration models
Software suite to create, edit, compose, or convert bitmap images.
IMOD is a set of image processing, modeling and display programs used for tomographic reconstruction and for 3D reconstruction of EM serial sections and optical sections.
iMOKA is a software that enables a comprehensive analysis of sequencing data from large cohorts to generate robust classification models or explore specific genetic elements associated with disease etiology.
instaGRAAL is a large genome reassembler based on Hi-C data (continuation and partial rewrite of GRAAL) and post-scaffolding polishing libraries.
Interactive assembly and analysis of RAD-seq data sets.
Efficient phylogenomic software by maximum likelihood.
calculate iRep replication rates from metagenome sequencing
The Integrated Rule-Oriented Data System (iRODS) is open source data management software
iSMC - The integrated Sequentially Markovian Coalescent
IsoQuant is a tool for the genome-based analysis of long RNA reads, such as PacBio or Oxford Nanopores. IsoQuant allows to reconstruct and quantify transcript models with high precision and decent recall.
Scalable de novo isoform discovery
ITSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences, which is commonly used as a molecular barcode for e.g. fungi.