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Hi, I'm a new user of the famous CANU. I wanted to assemble de novo a set of Nanopore gDNA reads (~800Mb) to get closer to a bacterial genome, which size is expected to be close to 4.5Mb.
I ran the f…
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I have previously used phyloseq to help analyse 16s data from illumina processed using QIIME generating biom file and using the ouitput of the core diversity analysis. I now have metagenomic data from…
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Hello,
Hello, I am trying to use Nanopolish v.11.0 on the Flux Linux-based operating environment at the University of Michigan to polish assembled contigs from Canu v1.8 of demultiplexed amplicons …
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Hi @jts & cia,
Recently, I happen to henerit a couple of sequencing runs done with the old R7 (I guess R7.3, but so far I cannot guarantee).
When I try to polish the contig of interest I have an…
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Hello, I am using Canu v1.8 on the Flux Linux-based operating environment at the University of Michigan to assemble contigs of demultiplexed amplicons generated from fungal genomic DNA using a Nanopor…
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Hi I have two questions,
I'm indexing, mapping the reads, and running nanopolish (v 0.10.1) (all of the information for them is the same directory). However, during nanopolish variants I am getting t…
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I am trying to correct some nanopore reads. My config file is called BaS_LR.txt and the following lings were modified:
PROJECT=BaS_LR
ONT_READ_LIST=BaS_LR_Seq.txt
GENOME_SIZE=5409120
THREADS=1…
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Hello, I am using Canu v1.3 on the Flux Linux-based operating environment at the University of Michigan to assemble contigs of demultiplexed amplicons generated from fungal genomic DNA using a Nanopor…
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I am computing a consensus sequence from short MinION reads (~1000bp at ~800X coverage).
My current command is:
```
canu \
-p test -d consensus \
-nanopore-raw 11_06_pooled.fastq \
gen…
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Currently Loaded Modulefiles:
1) psc_path/1.1 3) intel/17.4 5) gcc/5.3.0 7) java/jdk8u73
2) slurm/default 4) xdusage/2.0-4 6) gcc/7.3.0 8) canu/1.7
+ cd /pylon5/mc5fqip/…