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a lot of our ancillary documentation and workflows (genome-grist and spacegraphcats) suggests doing k-mer trimming of metagenomes, e.g. with trim-low-abund.
but, for gather in particular, this is n…
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Hi,
Thank you for the tool. I am trying to run PUPpy with test dataset before running with my original dataset. but I got the following error.
my command is:
`puppy-align -pr PUPpy/test/INPU…
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i have around 60 samples, that performed paired-end seq for metagenome, total ~400G clean data.
i have combine all forward reads and reverse reads, gained F.fastq,gz and R.fastq.gz. and than i run:
…
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Working on https://github.com/dib-lab/khmer/issues/998, using this command:
> ./setup.py nosetests --tests tests/test_scripts.py:test_load_graph_multithread
default args:
> args = ['-N', '4', '-x',…
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I am struggling to understand the useful looking `-F` option, which allows one to pass a fasta file from which k-mers are extracted and used as reads. I suspect I have misunderstood the manual:
```…
bede updated
7 months ago
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Here is my running code:
```
time metawrap quant_bins -b temp/bin_refinement2/ref4/metawrap_70_5_bins/ \
-t 48 -o temp/bin_arg/quant/summer \
-a result/megahit/summer.contigs.fa \
tem…
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Hi,
I have a question about the output from
`./dashing cmp –k10 -p5 -C -S24 --wj-exact reference_.fasta reads.fastq`
The output i.e. 0.0005 (says that 0.05% of the k-mers in the union are shared)…
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Hi!
The one2all/new2all give this information about the intersection sizes with a new sample:
s1: 100/150
s2: 200/300
s3: 50/1000
...
Is there any way to get more detailed information showin…
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$P$(observe k events) =
Here the parameter $\lambda = \frac{M}{S}$ is the expected number of hashes
for $M$ k-mers at a scaled of $S$.
$P$(k hashes for M k-mers with scaled S) = ${\exp(-M /…
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This is a feature request (as discussed with @bluegenes earlier today) to have the k-mers that correspond to the hash values also returned when doing a `sourmash sketch`. I was made aware of [sourmash…