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Hi there,
This is a semi-automated message from a fellow bioinformatician. Through a GitHub search, I found that the following source files make use of BLAST's `-max_target_seqs` parameter:
- [cons…
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Hello,
in my slurm config there is a partition with name "batch" containing 11 nodes with 20 cores/128G per node
i use the command
canu -p seabream useGrid=true gridOptions="-p batch" -d seabre…
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I have been trying to generate an hybrid assembly using Pacbio reads and Nanopore reads with CANU 1.8.
The slurm commands that i use is this :
```
#!/bin/bash
#PBS -V
#PBS -N Assembly_SE3
#PBS -…
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Hi,
I aligned some nanopore cDNA data using minimap2. It's human samples infected with a retrovirus. I aligned against a custom genome where the viral genome is used as an additional chromosome. Th…
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Hi canu team,
thanks for your work on this impressive pipeline. I hope this is the right forum for this question.
Our team is trying to some simple de novo assembly of a plasmid (and several plasmids…
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Hi,
I hope it's ok for me to ask for some guidance.
I'm assembling an apox 5gb bacterial genome.
Input Nanopore rapid barcoding kit, run on Minion. Deepbinner -> albacore -> porechop (trim only).
…
thsyd updated
5 years ago
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I managed to install canu successfully on ubuntu v18, however I am having issues trying to run the program.
This is how I start the program:
canu-1.7.1/*/bin/canu -p assem -d canu_outdir genomeS…
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I'm trying to understand what I can do about these errors:
```
$ tombo resquiggle /Volumes/Macintosh\ HD/Library/MinKNOW/data/reads/Reg_RNA_copy/fast5/pass/0/ /Volumes/Macintosh\ HD/Library/…
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Hi!
I aim to assemble a small fungi genome '(~25M)' using MinION long reads. The total input is ~7G bp datasets. I launched the assembly 12 days ago, and it has stayed at 'cormhap' step for 10 days…
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Hi,
I'm trying to assemble some amplicon sequencing data, but I keep getting the exit code 139. The amplicon is only ~700bp long, and I'm running this in an Ubuntu 16.04 virtual environment. The co…