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lbcb-sci / raven

De novo genome assembler for long uncorrected reads
MIT License
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mitogenome lost #44

Open JWDebler opened 3 years ago

JWDebler commented 3 years ago

Hi, I just ran raven over some of my nanopore data, and the assembly looks great, with one caveat, it lost the complete mitogenome. The same reads assembled by Canu lead to more fragmented contigs, but a tandem repeat of 3-4 mitogenomes. NECAT assembled the mitogenome into a single copy contig, but Raven seems to have discarded all the mitogenome reads as I cannot find any of the mito sequences anywhere in the assembly. Any idea what happend or how to find out? Cheers. Raven.Cereal file

rvaser commented 3 years ago

Hi, I'll check the cereal file, but please tell me the Raven version you are using.

Best regards, Robert

JWDebler commented 3 years ago

@rvaser Sorry, was away over the extended easter break. That was with version 1.5.0

rvaser commented 3 years ago

What is the expected size of the mitochondrial DNA? I inspected the cereal file but not sure what to look for.

JWDebler commented 3 years ago

It's 52504 bp. Would the sequence help?

rvaser commented 3 years ago

It could help :)

JWDebler commented 3 years ago

Here you go: mitogenome.zip

rvaser commented 3 years ago

@JWDebler, I inspected the GFA in more detail, there is a contig consisting of two reads that has 2.5x the mitochondrial genome. Raven did not print it as it is not circular and has only two connected reads. Sorry for the huge delay.