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ref #51
Mo -
so, khmer pre-allocate the memory even there's no need for it?
titus:speech_balloon: 9 minutes ago
Yes - after all, how do you know how many kmers there are if you haven’t read t…
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I'm not sure if this is an intended use case for Neptune, but I attempted to run the program with ~150 inclusion genomes (450 MB) and ~8000 exclusion genomes (32 GB) and it caused the program to crash…
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Some initial testing (human chr10) suggests that this yields a significant memory improvement when indexing (and a speed improvement too). On my laptop, indexing chr10 of human with `std::unordered_m…
rob-p updated
7 years ago
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Hello,
Many users of PanGenie might wish to use vg giraffe to align reads for short-variant calling, but use PanGenie for structural variant calling.
Inspired by PanGenie, the new haplotype-bas…
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This is just a conceptual question I'd like to figure out in order to better plan my future searches.
Assuming we have a query of length 100. Assuming (for simplicity) that no 31-mers within the se…
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I installed mitoz v3.6 using conda. The test run was ok. I wanted to generate mitogenome from a SE data. Below is my command,
```
mitoz all --outprefix PhoSp1_trimmed --clade Arthropoda --genetic_…
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Hi,
I had a query about calculating the genome size needed for the MACS --gsize option.
**Use case**
I shall be using genomes not listed in your documentation and so need to calculate the gen…
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I am assembling turtles mitogenomes and in some cases the output I obtain is a "Circularized genome", actually made up of 2 non overlapping contigs: in all these cases, the interruption is in correspo…
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Hello,
I'd be grateful to anyone who could give me some advice and/or help with the following. I am running a test dataset through idba_ud. The test dataset consists of ~10 bacterial species (metagen…
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Hello,
I was working on a single cell RNA-seq library which contains whole genome reads, not target-enrichment reads for immune profiling. I downsampled the library to 100k, 500k and 2million reads…