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medvedevgroup / SibeliaZ

A fast whole-genome aligner based on de Bruijn graphs
http://medvedevgroup.com/
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Are there a script to make circos plot? #16

Open baizixiansheng opened 4 years ago

baizixiansheng commented 4 years ago

After running the command: sibeliaz -t 10 genome1.fa, the output as follow: -rw-rw-r-- 1 shu shu 1.1G Jun 8 18:59 alignment.maf drwxr-xr-x 2 shu shu 38M Jun 8 18:59 blocks -rw-rw-r-- 1 shu shu 392M Jun 8 17:32 blocks_coords.gff ant the blocks/ file is empty. We want to get the circos input data, just like Sibelia- 3.0.7 ( but it could proceed input which is larger than 1 GB ). Thank you very much for your help.

iminkin commented 4 years ago

Hi @baizixiansheng ,

There is no such script now. We might add it in the future, but it is very likely that Circos plots made from large outputs will be way too convoluted and hard to read, though it depends a lot on the data. Please also note that SibeliaZ is slightly different from Sibelia: Sibelia is designed to generate large synteny blocks representing long common sequences, while SibeliaZ targets whole-genome alignment and generates much smaller blocks. To get synteny blocks from SibeliaZ, you have to run a postprocessing tool on its output.