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This could be useful for signatures that represent reads that have not been k-mer trimmed
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When using sbt_search with microbes.k31.sbt.json sourmash spits out an error. I calculated a signature for a single genome using sourmash compute -k 31 --scaled 10000 *fna.gz. The output of this works…
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I generated signatures from paired-end data like this:
```
rule calc_sigs_raw:
output: "outputs/sigs/raw/{sample}_raw.sig"
input:
R1="inputs/SRA/{sample}_1.fastq.gz",
R…
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It seems that 95% of my runtime on my (viral) application is in this step. The number of vertices is pretty small usually (thousands). But it can take tens of minutes. Coverage is high, so perhaps thi…
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Hi!
I'm super impressed with the speed of Shasta - and I'm taking advantage of its speed to explore parameters to optimize/maximize the size of genome assembly and longest assembled segment for ONT…
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I'm attempting to run a human genome assembly using Shasta on MacOS with the default parameters. However, I quickly run into the error below. My FASTA file has one-line sequences and no blank lines, s…
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Like, from within Python, how can I do the equivalent of
`sourmash compute ... --scaled 100 ...`
```
import sourmash_lib as sm
sig = sm.MinHash(ksize=16, n=1000)
# now scale
```
Thanks a …
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Hello! I'm using the container `docker pull quay.io/biocontainers/sourmash:2.0.0a7--py27_0` to run sourmash compute directly on `trim-low-abund.py` reads and am getting this strange error:
```zsh
…
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When I try to use CANU, I got the following error meassage:
```
ERROR: mhap overlapper requires java version at least 1.8.0; you have unknown (from 'java').
ERROR: 'java -showversion' reports:
…