Button for mobile navigation

Supported Applications


  • Description

    an efficient de novo trascriptome assembler for RNA-Seq data. It can assemble transcripts from RNA-Seq reads (in fasta format). Unlike most of de novo assembly methods that build de Bruijn graph or splicing graph by connecting k-mers which are sets of overlapping substrings generated from reads, IsoTree constructs splicing graph by connecting reads directly. For each splicing graph, IsoTree applies an iterative scheme of mixed integer linear program to build a prefix tree, called isoform tree. Each path from the root node of the isoform tree to a leaf node represents a plausible transcript candidate which will be pruned based on the information of pair-end reads.

  • Usage

    To list all executables provided by IsoTree, run: $ biogrids-list isotree Copy to clipboard
  • Installation

    Use the following command to install this title with the CLI client: $ biogrids-cli install isotree Copy to clipboard Available operating systems: Linux 64, OS X INTEL