Torbjørn Rognes

icon indicating a website link https://www.mn.uio.no/ifi/english/people/aca/torognes/ icon indicating an email [email protected]

icon company University of Oslo & Oslo University Hospital icon location Oslo, Norway icon location Developing tools for bioinformatics at Dept. of Informatics, University of Oslo and Dept. of Microbiology, Oslo University Hospital

Results 147 comments of Torbjørn Rognes

sintax: should the command accept the --minseqlength option?

Fixed in version 2.21.2, which has been released. Unfortunately I forgot to mention this in the release description.

fastq_pctid option for fastq_mergepairs

Yes, the vsearch `fastq_maxdiffpct` option argument should be equivalent to 1 minus the argument to the usearch `fastq_pctid` option. The `fastq_pctid` option must be a rather new option introduced in...

Add support for amino acid sequences

Thanks for the suggestion. In addition to what you have already noted, I believe some code is needed to detect the type of file (nucleotides/amino acids) as well. Also, there...

Add support for amino acid sequences

If you want fast amino acid searches perhaps Diamond, RAPsearch2, or [GHOSTZ](http://bioinformatics.oxfordjournals.org/content/early/2014/12/16/bioinformatics.btu780.short) would be appropriate? For clustering amino acid sequences I'm not sure.

Add support for amino acid sequences

Ok, we'll try to add support for amino acid sequences in a future version.

Add support for amino acid sequences

We have obtained funding to adapt vsearch to work with amino acid sequences. The work on this has just been started by @RonnySoak.

Add support for amino acid sequences

The work on this issue has been suspended due to lack of funding. Hopefully the work could be resumed again later. We will update the issue when we have more...

small unexpected difference in id3 similarity value

I guess the gap openings may be 2 in this case, as there is a large terminal gap on each side. That could explain the 98.7% value as 1 -...

Implement the search_global command

Thanks for the suggestion. We do not have any plans to implement cluster_otus. I'll look into it and see how much it will take.

Could vsearch Standardize the otu table and calculate the relative abundance of phyla, class, order, family and genus.

Thanks for your suggestion. We have not implemented these functions in vsearch yet. Unfortunately, we have limited capacity to implement new features and we do not have any plans to...