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Need to talk with Jonathan about public data - define metagenomes of most usefulness and easy to automate
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Dear OPERA-MS creators,
Thanks for the great tool!
I am attempting to assemble a **very** large and complex metagenome (~5e9 150 bp PE reads or ~ 8e11 basepairs short reads) with about 16 gbs …
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Hello,
I am working on identifying potential PULs in my metagenomes. I've run my dereplicated bins through prokka and dbCAN. I have uploaded the fasta file and prokka annotation to Geneious which …
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Getting metagenome files from accession numbers through NCBI, and then using BLAST to seach the metagenomes for B. infantis.
- [ ] manually look at results to see if they make sense
- [ ] Check wi…
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input:`!python run_Speed_up.py --contigs ComND.Sep_nonredundant.fasta`
outputs:
folder pred exist... cleaning dictionary
Dictionary cleaned
Creating Diamond database...
diamond v0.9.14.115 | by B…
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there are three ways to do this.
* mapping based: map reads, call variants, build a variant call file (VCF), estimate ANI from VCF SNP calls.
* mapping based: create a new consensus genome based o…
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Hi,
First of all, thanks for developing this tool!
I have a few metagenomic samples from which I've estimated the number of couple of reads mapping in proper pair to the SSU rRNA genes present in …
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Is there a way to use sourmash to compare the presence/absence of species from multiple metagenomes? I would like to use “whats in my metagenome” from [this tutorial](https://sourmash.readthedocs.io/e…
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Dear author,
Thanks for your excellent work. I have some VLP enrichment samples from the animal gut. When I use the tool, how to select the parameter "--enrichment_preset". The default is "human",…
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calc-hash-presence.py from [pangenome-hash-cor](https://github.com/ctb/2024-pangenome-hash-corr), does not yet allow me to compare protein sketches instead of nucleotide sketches.
I'd like to comp…