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Hi,
I am currently trying to implement the metaGEM pipeline for the assembly and metabolic reconstruction of eukaryotic (particularly fungal) genomes. I was wondering if EukRep has been integrated …
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I'm just using 3 input fastq files with 10k reads each, as just a test.
My workflow:
```r
config_file = FLAMES::create_config(outdir, type = "sc_3end", do_barcode_demultiplex = TRUE)
sce = …
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Hi sir,
While I was querying one genome against ~2000 genome, it was very slow. I checked back the paper on 90k prokaryotic genomes and found indexing would take the majority of the runtime, so I w…
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Hi,
During the simulation of ultra-long ONT reads, an error was encountered: "fastq is too long. Max acceptable length is 1000000."
Will the program be updated?
Best.
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Why is there no legend in the genome circle diagram? How to add legend ?Thanks!
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In recent runs against the latest NCBI dataset of Listeria, we've observed large discrepancies between RabbitTClust and NCBI clustering results. Here're a few examples.
1. When distance threshold < …
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Hi,
Thanks for CLEAR.
I am in troubles using CLEAR and looking for solutions. I need your help and this is the error log.
```bash
###Parameters:
Namespace(bowtie1='/home/ionadmin/likun…
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Hi, thank you for this approach, absolutely fascinating! I'm hoping to use this in a workflow to assess and triage eukaryotic genome annotations using FoldSeek. The range of protein sequences can be s…
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Hi @glennhickey:
I have got the vcf result from the minigraph-cactus pangenome pipeline. how can I get the coords of the SVs in the query genomes since there are only coor…
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Hello,
I am running Clinker on a server (installed via conda) for five genomes (from the same genus); gbk files were downloaded from GenBank. I use the following command:
`clinker ./genomes/*.gbk…