vsearch

vsearch copied to clipboard

As a follow-up on issue #545, here is a list of `--userfields` options available in `usearch` (see [userfields](https://drive5.com/usearch/manual/userfields.html)), but not in `vsearch`. Starting with the most important, in my opinion:...

frederic-mahe

control of 2 separate randseed events in sintax

10

I see two places where sintax would need a random seed: 1. when a subset of kmers are randomly sampled from the query sequence. 2. when these kmers match equally...

todd-desantis

More than 7 levels in sintax

4

At the moment the sintax runs only work with default 7 levels, going from `kingdom` to `species`. It would be great if it could also take more levels containing strains...

lokeshbio

Why FASTQ quality value above qmax is treated as Fatal error?

5

When I used `--fastx_filter` to trim FASTQ files (seeming like a very easy task), ``` $ vsearch --fastx_filter in.fastq --fastq_stripleft 20 --fastq_stripright 20 --fastaout out.fa ``` I encountered Fatal error...

billzt

There should be an option to output the reason why merging failed with each pair of reads when using the `fastq_mergepairs` command. I think usearch has an option for this....

torognes

After combine two datasets together to recluster, some of the abundance of high-abundant OTUs were reduced dramatically.

2

I have two datasets A and B, where there is a high-abundance OTU (id: OTU_54) in dataset A. In order to compare the abundance of OTU_54 in the two datasets,...

peiyaohu

Chimera detection --uchime_ref unexpected behaviour

6

Hello, I've been using --uchime_ref to identify chimeras providing a list of reference sequences in FASTA format. I noticed that vsearch does not report match with highest score when there...

nvucic

--weak_id not working

7

I am testing the --weak_id parameter for usearch_global, but it does not appear to be working. When I run a query with --id 0.85 I get ~10,000 of my query...

dleopold

Adapt for RISC-V

2

VSEARCH could be adapted to run on [RISC-V](https://en.wikipedia.org/wiki/RISC-V) systems. The SIMD code would need to be translated to the vector capabilities of this platform. Until we have actual RISC-V hardware...

torognes

unexpected behaviour - v 2.28 sintax chooses first sequence when not classifiable

4

command: **$ vsearch --db UNITE10.fasta --sintax refs.fasta --tabbedout refs_sintaxonomy.tsv --sintax_cutoff 0.8 --sintax_random** **vsearch v2.28.1_linux_x86_64, 251.2GB RAM, 96 cores** produces this output for the first 5 sequences (these are not closely...

givdieri