BRIG is a cross-platform (Windows/Mac/Unix) application that can display circular comparisons between a large number of genomes, with a focus on handling genome assembly data.
Please cite the BRIG paper if BRIG is used to generate figures for publications: NF Alikhan, NK Petty, NL Ben Zakour, SA Beatson (2011) BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons, BMC Genomics, 12:402. PMID: 21824423
- Images show similarity between a central reference sequence and other sequences as concentric rings.
- BRIG will perform all BLAST comparisons and file parsing automatically via a simple GUI.
- Contig boundaries and read coverage can be displayed for draft genomes; customized graphs and annotations can be displayed.
- Using a user-defined set of genes as input, BRIG can display gene presence, absence, truncation or sequence variation in a set of complete genomes, draft genomes or even raw, unassembled sequence data.
- BRIG also accepts SAM-formatted read-mapping files enabling genomic regions present in unassembled sequence data from multiple samples to be compared simultaneously
Thanks for the nice program. I have a problem when mapping coverage Graphs. When CGview parses the XML file first I encountered an out of memory error: "GC overhead limit" which I avoided with -XX:-UseGCOverheadLimit but then instead i got the memory error "Java heap space". I want to run coverage mappings for 20 genomes of ~6,5 Mbp so it is quite a lot of data to render, but I have tried allocating more memory (15gb) and still get the error. Do you have a suggestion for solcing the problem? I'm running BRIG on a UNIX server, tunnelling java.
Thanks for software and updates.
Great interface and easy to use.