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Hello and thanks for the awesome tool.
I have a question, I see you efficiently introduced a method to plot and represent beta-diversity between samples (dissimiliarities).
I was thinking, what …
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Hi,
we recently sequenced a batch of 19 fungal isolates. I tried to assemble the genomes a few different ways (simplex + duplex or simplex corrected only) in order to figure out if there is still a…
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Hi,
learnErrors and dada with multithread = TRUE and removeBimeraDenovo result in ‘caught segfault’ error, please see the details below. With default multithread = FALSE learnErrors and dada work a…
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Hey,
I'm in the process of creating a wrapper crate for Rust bindings (https://github.com/RagnarGrootKoerkamp/libsais-rs/blob/master/src/lib.rs), so that we can easily use `libsais` for bioinformat…
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I'm currently testing linclust using the easy-linclust workflow with very small datasets (100 / 1000 sequences). Each sequence is a nucleotide sequence, on average, 3000 basepairs long. So using 20 …
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Hi,
Firstly thank you for creating such a great resource. I have two questions (using v1.5):
1) I am trying to genotype SVs using identified by manta (only SVs), when following the steps and usi…
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I'm interested in finding the location of kmer which are present twice in a genome fasta file.
I collect these kmers using kmc and transform the kmc dump to fasta before running klocate.
When I …
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I'm assuming we'd be using 2 bits per bp. There's a couple of common encodings, but I want to suggest
```
A -> 00
C -> 01
T -> 10
G -> 11
```
There's a couple of benefits:
1. These are the 2nd…
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I ran kgwasflow without issue from the latest version, but I noticed a potential problem. In my dataset, I have 79 samples with no missing data for phenotypes. This is reflected in the input files and…
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Hi Mike,
Hope all is well with you
I'm revisiting our GenomeScope analyses with cleaner reads and was curious about a trend I see in many papers. As well as looking at other k-mer based assembly ev…