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When we specify multiple assemblies with `getset`, agc seems to buffer all the output in memory. If we pipe the agc output to another program (e.g. ropebwt3) that consumes the output slowly, agc will …
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Hello, arangrhie,
Merqury has proven to be an excellent tool for evaluating genomes.
I currently possess a haplotype-resolved genome from an autotetraploid species, which includes four haplotype…
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Dear CAMISIM team,
I am starting to try and use CAMISIM for a bunch of projects we have, but wonder if all of them will fit. For instance, is it possible to use CAMISIM for simulating amplicon sequ…
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Thank you for providing this tool! I am curious if there is an established cutoff or threshold for determining similarity during analysis. Specifically, have you tested how well the tool can discrimin…
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When dereplicating sequences, it is crucial to cluster genomes that significantly overlap each other (i.e., high bidirectional coverage) to avoid clustering sequences where one is entirely contained w…
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Dear PBSIM3 maintainers,
I am YU Zhejian from the Zhejiang University-University of Edinburgh Institute. Our group has been using PBSIM1/2/3 to simulate long-read RNA-Seq reads (with [YASIM](https:…
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Hi,
I am struggling to workout and estimate minimal resources to run cactus for 100 genomes mammal size.
I can use CPUs, GPUs but I need to estimate amount of resource for an amount of time (project…
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How does `fcs-gx` uses memory? Does it load the entire DB into memory every time? If not, is there a way to estimate the approximate memory usage of `fcs-gx`?
According to the README file, `fcs-gx`…
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# Summary
Users cannot view reads. The IGV panel opens, but the tracks do not load. Inspecting the browser console reveals that an HTTP request for reference files returns with a 403 error.
The HT…
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For your genomescope 2.0 it is mentioned as well that it is only suitable for genomes with even ploidy (2xp). However, in the publication it is clearly stated that tetraploid and pentaploid genomes we…