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Hi,
I'm trying to use velvet + metavelvet to assemble a metagenomic dataset but when I try to construct k-mer hash table with an hash_length of 51 (as suggested in the MetaVelvet pipeline) I get the f…
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Hi,
I am using the following command:
`./canu -useGrid=0 -p BC05 -d /n/scratch2/dct7/Run11_Canu/BC05_AC347 genomeSize=9000 contigFilter="2 1000 1.0 1.0 2" -nanopore-raw /n/scratch2/dct7/Run11_C…
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Hi All,
I'm new to running Canu and quite a novice at using terminal commands. I managed to get Canu installed on an iMac that I use for Nanopore sequencing. I am looking to run an assembly with Ca…
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I'm running [this workflow](https://github.com/czbiohub/reflow-workflows/pull/3/files#diff-8f97322b36ae1295dd18955efe81f974) which uses the command `trim-low-abund.py` from [khmer](http://khmer.readth…
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`swig/BloomFilter.i` is defining an interface to `insert()` and `contains()` methods accepting `const char*` but `BloomFilter.hpp` doesn't contain those definitions, only ones involving `size_t` refer…
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Long running tasks are terminated on our login nodes, so I am trying to generate the sbatch scripts with `useGrid=remote`. Even though Canu correctly detects my slurm configuration, it just starts run…
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Hi guys,
I am running Canu v1.7 +0 changes (r8692 c9ef9219a265e0bbe3a311cca7d28aa02b7517d3) and while I get an assembly I do not get any corrected reads. My command is
`./canu -useGrid=0 -p BC6…
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Hey,
I tried to understand which kmers are counted by squeakr-count. I noticed that only the first k bases from the input reads are counted, and the kmers further down the reads are discarded. Also…
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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
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I have a similar issue like #546 and #718
I installed canu 1.7 on an ubuntu (16.4) workstation. I have a 1G assembly length but with a very low nanopore reads coverage (5X).
This is the command I …