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I did not finish my run and stop at 4-unitigger.
I get the error files as following:
unitigger.err:
```
Graph error threshold = 0.105 (10.500%)
Max error threshold = 0.105 (10.500%)
…
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Dear Canu developers,
many thanks for providing this assembler. The assembler works and unitigs were generated.
To have a closer look at the unitigs and the aligned PacBio reads at the unitig I was…
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Hi All,
How can I tell canu that it should not make the unitig when only two reads overlap - I know that I can filter out unitigs already made, but as I have seen I have several cases when contigs no…
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I'm trying to assemble a circular mitochondria at the moment and getting a little frustrated that Canu isn't picking up on the circular aspect of it. I note that the Geneious assembler implements circ…
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Hi,
I have talked a bit with Brian about this, but thought it was just as well reporting it as an issue.
Version 1 of unitigs reports this:
```
-- Found, in version 1, after unitig construction:
--…
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Graph error threshold = 0.050 (5.000%)
Bubble error threshold = 0.062 (6.250%)
Merge error threshold = 0.037 (3.750%)
Repeat error threshold = 0.050 (5.000%)
Minimum overlap length = 3000 bases
…
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I am trying to assemble a ~620Mb plant genome (essentially haploid, 35% GC) using a 91x PacBio dataset. The first assembly with **CANU** v1.3 (using `corMhapSensitivity=low`, other params are default)…
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Hi, Jason and Chris,
See contig_to_graph.py
I inadvertently changed line 162 of:
https://github.com/PacificBiosciences/FALCON/blob/master/falcon_kit/mains/graph_to_contig.py
from:
if type_ == "si…
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Hi,
I'm getting an error code on what looks like k77 step of a large assembly.
cmd: /home/ubuntu/megahit/megahit_sdbg_build read2sdbg -k 27 -m 2 --host_mem 80000000000 --mem_flag 1 --gpu_mem 0 --ou…
adina updated
7 years ago
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Hi @noporpoise,
I'm running mccortex building and cleaning on a bunch of samples from the ENA and a small percentage are failing on the cleaning step without much information as to why.
Here's…