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I would like to extract the translated orfs after running a translated search (proteins against nucleotide) and `gff2db` followed by `translatenucs` seemed like the way to go. However, MMseqs2 has bee…
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Whenever I try to select Prokka as a tool for finding ORFs, MetAMOS uses FragGeneScan. After reviewing the code of `runPipeline`, `findorfs.py` and `findscforfs.py` I found out that prokka is not on t…
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### Feature Request
We want to switch over from nextclade 2 to nextclade v3.
### Solution
1) re-factor the nextclade json parser script to accomodate the new json format.
2) update the wdl to a…
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## Expected Behavior
I try to use easy-linsearch and linsearch but both have same issue : empty files
First, I have try easy-linsearch with the line :
"$ mmseqs easy-linsearch /work/cbelliardo/6-en…
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## Expected Behavior
k-mer similarity threshold: 145
Starting prefiltering scores calculation (step 1 of 1)
Query db start 1 to 469186
Target db start 1 to 579233
[=============================…
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Hi @bbuchfink - I read your preprint and am excited to try out the clustering workflow on metagenomic data. However, I wasn't entirely sure if Diamond2 can select the longest sequence as the represen…
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Sometimes, the best microcin hit doesn't end up too near the CvaB, which may be fine. I think it would also be useful to report hits from the filtered microcin peptides that are three orfs up or downs…
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How do you output a protein fasta (.faa)?
Also, I keep getting an error for start/stop options?
Do I use prodigal on the orfs this calls?
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Hi,
I got the following error while testing viga using my own viral contigs:
```
...
Detected 8 ORFs in CONTIG_996.fna
Detected 12 ORFs in CONTIG_997.fna
Detected 8 ORFs in CONTIG_998.fna
…
housw updated
5 years ago
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I am considering looking for overlapping genes in some viral metagenomes I obtained. I am not interested into the overlaps themselves but more into genes that I would have missed because of big overla…