Issues with synteny blocks coverage is too low

mikolmogorov / Ragout

Chromosome-level scaffolding using multiple references

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Issues with synteny blocks coverage is too low #28

Closed isaurabhkr closed 5 years ago

isaurabhkr commented 6 years ago

Hi, I'm trying to assemble contaminated read data (from two different bacterial species), and in many cases, I'm getting error "synteny blocks coverage is too low." Can you please tell me what we can infer from this? Is there a problem with the references, or we don't have enough reads/fragments to stitch into scaffolds using the breakpoint graph algorithm that Ragout follows.

Thanks

mikolmogorov commented 6 years ago

Hi,

Could you send me the log file (ragout.log)? The low block coverage might either be because (i) the genomes are too divergent so they don't share enough homology or (ii) the length of the genomes is significantly different. Does any of this apply? Also, what is N50 of assembly?

mikolmogorov commented 5 years ago

Closing due to inactivity