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The catlas output files are described at a couple places. I found [this page](https://spacegraphcats.github.io/spacegraphcats/01-running-spacegraphcats/) the most comprehensive. However, the descripti…
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Two possible additions
### An equivalent to the `-m` option in ska1:
> Finally, the base call for the middle base in the split kmer is filtered to remove any bases where the minor alleles are foun…
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I have a workflow which uses kmc to count all kmers in an extremely large dataset of about 250,000 fasta files. The workflow was originally built with v3.2.1 of kmc, but stalled when I updates to v3.2…
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Hello,
I have a dataset where the KMC database is 1.4 Terabytes. I have been using the GetCountersForRead function, but as currently implemented this requires the database be loaded in random acces…
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When filtering reads, if the reads are paired, it would help to be able to say either "keep both reads if one passes the filter" or "drop both reads if one fails the filter", while preserving the read…
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Index made by gramtools `build` is memory hungry.
Two things:
i)Disk serialisation of index is significantly smaller than in-RAM
For eg on TB dataset:
(yoda: /nfs/leia/research/iqbal/bletche…
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If ANVIO can pass in the contig lengths then we can filter and only cluster with say contigs > 1000bp. The rest we can still assign to clusters based on responsibilities.
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Hi,
We try to list all possible kmers from a pair of fastq files using:
```
kmc \
-k31 -m128 -ci1 -cs4294967295 -cx1e13 -t36 \
-jOutput.json \
@files.lst \
test.kmer.output \
`pwd`/kmc…
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Hi,
Thanks for this wonderful tool! I'm writing to ask a question about the color of unitigs. I found about 3% of the unitigs created from Bifrost is of no colors. Is this because these unitigs do …
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Hello, how can I use the .fa file and the .vcf file to generate a .gcsa2 format or a .graph file? thanks a lot!