This project is archived and no longer maintained.
TIGRA
| Overview | |
| Description | TIGRA: A Targeted Iterative Graph Routing Assembler for Breakpoint Assembly |
| Development Information | |
| Language | C++ |
| Current version | 0.3.7 |
| License | GPL v3 |
| Status | Archived |
| Last updated | 2013/06/29 |
| References | |
| Citation | Chen K, Chen L, Fan X, Wallis J, Ding L, Weinstock G. TIGRA: A Targeted Iterative Graph Routing Assembler for breakpoint assembly. Genome Res. e-Pub 12/4/2013. PMID: 24307552. https://doi.org/10.1101/gr.162883.113 |
| Help and Support | |
| Contact | Ken Chen |
Tigra is a computer program that conducts targeted local assembly of structural variants (SV) using targeted iterative graph routing assembly (TIGRA) algorithm. It takes as input a list of putative SV calls and a set of bam files that contain reads mapped to a reference genome such as NCBI build36. For each SV call, it assembles the set of reads that were mapped or partially mapped to the region of interest (ROI) in the corresponding bam files. Instead of outputing a single consensus sequence, tigra_sv attempts to construct all the alternative alleles in the ROI as long as they received sufficient sequence coverage (usually >= 2x). It also utilizes the variant type information in the input files to select reads for assembly. Tigra is effective at improving the SV prediction accuracy and resolution in short reads analysis and can produce accurate breakpoint sequences that are useful to understand the origin, mechanism and pathology underlying the SVs.
Decode SV breakpoints from a TIGRA contig. Use the TIGRA-ext pipeline at https://bitbucket.org/xianfan/tigra-ext
On a unix shell, use tar -zxf to untar the following packages.
The most updated version: available at bitbucket
Source code (39 Kb)
Test data