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Do you need to create databases or is there a better option?
I created a database for copepods:
```
makeblastdb -in ../blastpacope/genomas_copepods/ncbi_dataset/data/db_all_copepods.fna -dbtype…
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Hi, I was running atlas on a metagenomic dataset (CD151) and ran into this error.
```
rule run_das_tool:
input: CD151/binning/DASTool/metabat.scaffolds2bin, CD151/binning/DASTool/maxbin.scaf…
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Hi,
I have run flye 2.8-b1674 on a 6 Gb, diploid genome with presumably high amounts of repeats. The coverage of my PacBio data is approximately 50 x. As a result the final assembly is 3.9 Gb in si…
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Hello, it's me again.
After finally putting SQMtools to work thanks to your help, I find myself again facing some problems (or at least I think so). As I said on my first topic here, I'm working wi…
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Hi,
I looked through the suggestions and tried using --meta parameter as well as --asm-coverage, but somehow no assembly is getting formed. I have raw metagenomic data from oxford nanopore. I am gett…
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This is focused on metabarcoding studies, but metagenomics is also briefly mentioned. I guess adding information from metagenomics datasets is another challenge, maybe there could be some mention of p…
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Hi all,
I used your excellent software call for taxnomy, and I found that there is an unknown bacteria particularly high in my case samples.(meta_mOTU_v25_12476).
Then I went to binning, and I ass…
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Hey, I'm fascinated by how fast minimap2 is. I would like to use it to calculate Average nucleotide identity for metagenome assembled genomes or normal genomes to group them into species (95% identity…
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I found a minor problem in the README while setting up nf-core/mag for offline use:
in the **cat_db** section, this URI is not working for me (and if the * was intended, is causing a md format chan…
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Hi Xavier!
I am wondering whether we can use ClonalFrameML to calculate recombination to mutation rates of metagenome-assembled genomes (MAGs). I see that in the literature, people mostly used your…