Comments (9)
What is the NextDenovo version you used? and how about the genome size, heterozygous rate, and repeat content? I do not suggested use corrected data, because NextDenovo will correct the raw data and filter some low quality or unuseful seeds. BTW, Could you provide the co-line pictures?
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How about the assembly result using canu?
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I can not see the figures, if you have problem to upload the figures to github, you can send the figures to my email: huj_at_grandomics.com. BTW, could you provide the configure file and the assembly log (the last step log)?
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I find your seed_cutoff is very short? How many data you used to do the assembly?
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Your data is not enough for assembly using the currently version of NextDenovo with default options, because all default options are optimize with 60-100x nanopore data. So it will produce an unexpected assembly result. But if you still want to use NextDenovo to do the assembly, you can try to use the option correction_options = -b
and change -k 30
in sort_options
and than rerun all pipeline, while I can not guarantee you can get a good result. You also can try to other assemblers. I will release a set of preset parameters for assembly with low-depth data in the future.
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Related Issues (20)
- Assembly is running around a month and going strong - or is it stalled? HOT 15
- about the ParallelTask for the nextdenovo HOT 1
- NextDenovo Parent Job Failed, No Error, Subtasks still running HOT 1
- Low performance with highly repeated regions HOT 1
- non-zero exit status 137, error info: . - assembly still finishes though HOT 1
- Unable to run test data on macOS HOT 4
- Samtools sort out-of-memory HOT 1
- Segmentation fault (core dumped) at 03.ctg_graph/01.ctg_graph.sh.work/ctg_graph0 HOT 1
- Can you run nextDenovo without a config file? HOT 1
- TypeError: unsupported operand type(s) HOT 2
- long time for assemling genome HOT 6
- Can I assemble a gap free genome using only regular ONT data? HOT 1
- telomeres getting lost HOT 6
- [4501 ERROR] 2023-06-13 22:29:40 the input data is insufficient for an assembly. HOT 3
- No assembly file after running NextDenovo HOT 1
- sort_align step erro HOT 1
- Does NEXTDENOVO filter the contig before output? HOT 2
- Error: db_stat failed ? HOT 1
- ERROR:the input data is insufficient for an assembly HOT 3
- Question about error rate for correction HOT 1
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