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Is there a way to create a completely new database and non-NCBI taxonomy for that database? I am primarily interested in using something like GTDB, which has a genome download and taxonomy tsv file av…
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I'm using getorganelle to extract mitochondrial genomes from insects. I first do an assembly using SPAdes (because we use that output for other downstream tasks anyway), and then I run get_organelle_f…
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Hi! Thanks for a great tool. I was wondering if you could implement an option to remove a contig or a list of contigs when calculating the stats. Sometimes I have bacterial contaminations, or the mito…
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Can't get fasta_to_features.py to run on contigs containing N's. Is there a workaround for this?
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Hello,
I get the following error:
usage: vamb outdir tnf_input rpkm_input [options]
vamb: error: unrecognized arguments: --jgi output/mapping/cobinning/bam_contigs_depths.txt
This is possibl…
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Hello! I'm using OPERA-MS to assembly NGS and nanopore reads.
the key parameters were set as ''--short-read1 {R1} --short-read2 {R2} --long-read {TGS} --out-dir {out_dir} --no-polishing -…
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Thanks for your excellent tool.
Previously I used vamb 3.0.2 for data analysls.
Currently I'm trying to run the latest version of vamb4, but unfortunately met such Runtime Error which I haven't figu…
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Hey,
Currently the visualisation seems to have some errors and provides no output.
Best,
Tom
`mobmess visualize -s test-contigs.fa -a test-contigs-annotations.txt --contigs $contigs --thread…
thh32 updated
2 weeks ago
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### Description of the bug
I really want to run this pipeline, however, I am facing several issues. First, with spades memory, I ran the assemblies out of the pipeline, and I tried to run the pipelin…