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My database contains lots of genomes, over 15k bacterial and all fungi from genbank, so it is unlikely for a result with 0 overlap. Also I had already run Clark and Kaiju and both return good results.…
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Hello, I've used SPAdes to assemble my metagenomic datasets however two of my samples are getting stuck in the exact same place repeatedly. I was able to assemble all my samples using megahit without …
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I using the latest kmc code but i can't count kmer on fastq file. It work on fasta
```
$cat r1_test.fq
@0|Chromosome|4051100|4051286/2 BX:Z:CGACACGGTTTGGGCC
AAACCCAACCAC
+
FFFFFFFFFFFF
$kmc …
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dear will-rowe,
HULK is concerned about the k-mer frequency as described in your paper. I find that a minimizer hash value cannot be added into the minimizerSketch when it is contained in the sketc…
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**EDIT I guess it would help if I were to read the publication to see especially the figures on time and amplitude domains' effects on base identity.**
Hi, thank you very much for developing this t…
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Is there a way to retrieve a list of the most contributing features (i.e., k-mer sequences) and their associated weights? I have attempted to pull them by using the sklearn.feature_extraction module t…
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Hi MashMap,
Hope this email finds you well.
Just wondering is it possible to indicate a specific window size? Or, is it automatically calculated based on segment length?
From the "mashmap -h"…
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It would be interesting and useful to extract k-mers when reading assembly sequences (FASTA), and perform some simple dimensionality reduction (such as PCA) afterwards to build a meaningful scatter pl…
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Hi @mourisl,
It was exciting to meet you at CSHL and I appreciate that you took some time to implement the feature we discussed.
I gave it a try this morning, and saving the trusted k-mers file …
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Hi,
I am a molecular biologist. Briefly, I am working on a non-model species, with no genomic data. I have some Genotyping-By-Sequencing data from different populations and I want to use npGeno to …