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Tried assembling H37Ra Tuberculosis genome from a MinIon run using
canu -p H37Ra.canu -d canu genomeSize=4.4m -nanopore-raw ./ useGrid=false gnuplotTested=true stopOnReadQuality=false
and
Canu s…
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I encountered the following error when trying to build from Docker:
The command '/bin/sh -c git clone https://github.com/marbl/canu.git && cd canu/src && make -j && cd -' returned a non-zero code:…
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I am running masurca v3.2.3. I got an error at celera assembly step. The log report is below:
[Wed 23 May 17:16:57 BST 2018] Processing pe library reads
[Wed 23 May 17:34:23 BST 2018] Average PE r…
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I'm using MinION 1D fastq file which contains an amplicon.
I should note that the PCR amplification was probably not as specific as we'd wish.
Either way, it's a rather large file,
Number of rea…
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[example.tar.gz](https://github.com/gringer/bioinfscripts/files/1114987/example.tar.gz)
Dear David,
I have been in touch with your scripts to manipulate raw nanopore sequences (twitter, such a ni…
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We downloaded part of this dataset (I think chr 20 only), and I am seeing some flow cell names which don't appear in the README: `FAB38968`, `FAB42483`, and `FAB46682`. (I'm also missing `FAB42483` en…
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Thanks for developing Nanopolish and for your help. I’m trying to use Nanopolish to call variants from MinION reads of amplicons (~2Kb long; ~ 50,000 reads each) and am getting an error. Here is wha…
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Hi,
I have been attempting to use nanopolish index on a 1D nanopore dataset (FLOMIN-107) basecalled using Albacore 2.1.3. The run crashed with a core dump and the error message displayed below. I h…
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Hello Sergey,
My canu run doesn't output genome assembly. It only generated correction folder. It seems to me that trim and assemble were aborted, but no error was thrown in the log file.
This…
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Hi,
I'm starting to use MinION sequencing to sequence ~450-550bp amplicons. This is done to set up a sensitive assay to get a complete viral genome in the end (with overlapping amplicons). I would …
BOM86 updated
6 years ago