Assembly missing ~300 kbp

[herber4]

Hello Spades,

My assembly is missing about 300 kbp in the final assembly. I am using paired end reads with the --careful option, but have tried many other options for optimizing the assembly including the incorporation of reads from multiple different lanes.

What can I do to increase the accuracy of the genome size in my assembly?

Best,

AAH

[asl]

How have you found that something is missing?

[herber4]

In comparison to the published reference genome, and assemblies conducted on the same reads using other assemblers, the assemblies output by spades is short about 300 kbp

[asl]

So, have you checked that the region is question indeed has some read coverage? Will you please post your spades.log file

[herber4]

spades.log

The ref genomes are ~4.2 kbp per GenBank

[asl]

Well, judging from the coverage histogram, the genome size is ~3.9 Mbp. I would suggest you to use --isolate mode and skip the read error correction (though, it would be so for --isolate).