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Hi, I am trying to calculate the kmer profile of this 5.0 Gb genome. Here's the command:
kat comp -t 32 -m 17 -o genome1VSgenome2 -h 'fastq1_R1.fastq.gz fastq1_R.fastq.gz fastq2_R1.fastq.gz fastq2_…
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I have a few WGS samples (matched T/N) at 80X with relatively high purity and have matched FISH showing ecDNA with the target gene. I ran amplicon architect suite with suggested inputs and the output …
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Hi Gabriel,
I'm trying to run schmutzi.pl and I am getting the following error:
```
running cmd endoCaller -seq b07_npred_1_endo.fa -log b07_npred_1_endo.log -name MT -qual 0 -logindel 50…
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Dear authors,
I remember asking this question before, but when looking back, I still am having some last doubts I was hoping you could help me with.
This is a summary of organism, abundance.tsv,…
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hi,
I have read the genomescope and genomescope2 article, but there is no specific method and principle in it, so i still confused it!
If I want to study genomscope the rationale behind it, can you…
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Hi~ Thank you for this wonderful work, i would like to know about an issue i came across.
KIR3DL3, KIR3DP1, KIR2DL4, and KIR3DL2 are four frame kir genes which in principle every individual should h…
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The description of point 3) CNV discovery is written unclearly.
In Required arguments, the descriptions are confused for me.
"-- output" does not refer to the bed file but to the folder where th…
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First of all, thank you for this and other NextStrain packages! They are making the process of visualizing my project significantly smoother.
### Current Behavior
I'm not sure if this is expected …
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I have just run purge_dups using the manual pipeline (so that I could set arguments like '-x map-ont' for minimap2). My input was a nematode genome assembly of 155 Mb and 50x coverage with Oxford Nan…
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the low complexity filter has a fixed default 30%
that is priobably ok for genomes with 50% GC
but if my bacterial genome say has 78% GC, then statistically 30% might throw away too much
might be c…