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Hi,
I'm having difficulty clustering using profiles when following the instructions in the wiki. Specifically I'm referring to this section:
```
# extract consensus sequences from profiles
…
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Hi,
I am trying to get the taxonomy of several contigs present in a multi-fasta file, but I'm having some issues with the `easy-taxonomy` command, as it is has not completed the assignment of about …
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I am trying to build an index for NT (NCBI non-redundant nucleotide database). I am using a machine with 96CPUs and 756GB, I have tried:
`metagraph build -v -k 31 -o graph -p 96 --disk-swap /mnt/tmp…
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we are using GTDB taxonomy because -
* GTDB provides a nice collection of representative genomes
* GTDB provides species clusters based on ANI, which matches the approach used in charcoal
* the g…
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Hi @ilyaminkin,
We've run into another minor issue that we _think_ is a bug. I wanted to report the behavior here to get your feedback on it. Basically, what we're seeing is that, for a small n…
rob-p updated
7 years ago
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Querying human reads to the human genome ([ref](ftp://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/annotation/GRCh38_latest/refseq_identifiers/GRCh38_latest_genomic.fna.gz)) is very slow (~500 RPM, a **1000x…
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Interesting new tool from NCBI that they're applying to the SRA data!
(Text found via Analysis (alpha) tab, [linked from here](https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=ERR929453))
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Sometimes, Ray Meta seems stuck. The log output looks as follows:
```
...
Rank 7 computing contig abundances [63043/130531] [118/118]
Rank 77 computing contig abundances [62815/130236] [1/118]
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over on twitter, ben woodcroft [asked](https://twitter.com/wwood/status/1562255085463171073) if/when sourmash would report the relative abundance of each genome, taking into account shared k-mers.
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To interpret the learned codes it would help to have the following visualizations:
1. distance matrix clustering for all TFs. Do probes from like families cluster together?
2. Visualizatio…