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torognes
Versatile open-source tool for microbiome analysis
Seeing false full length alignments that show 100% identity to stretches of Ns. vsearch v2.14.1_linux_x86_64 ``` vsearch --usearch_global nano_reclust.fa \ --db blastoNCBI_120919.udb \ --userout nano_reclust.vsearch \ --userfields query+id+alnlen+qcov+target \ --output_no_hits...
I've been using vsearch a lot recently to group sequences with `--cluster_fast`. In my specific case, I've been ending up with many singletons (10,000s at a time) that get output...
This issue has a low priority. I am exploring some corner cases when changing the identity value default definition. With `id3`, I've encountered a case with a small difference between...
Dear @torognes, Using the sintax xlassifier I noticed that the algorithm in case of multiple identical best hits only outputs the first hit irrespective of the hits after that. This...
Auto-completion is a functionality that presents possible options when users press the `tab` key while typing a command or options for that command. There are plenty of guides on how...
The `--relabel @` option will relabel sequences with a prefix constructed from the initial part of the file name, truncated at the first underscore or period.
SIMD-vectorization of global alignment of one query vs one target sequence. Should use the striped approach of Farrar (2007) or the vertical vector approach of Rognes (2000).
Hi! I have a question regarding handling of sequences with different length. I usually align sequences with a fixed identity cutoff of 97% and, depending on the sample, different read...
I am running the following command: ``` vsearch --usearch_global $query --id 0.9 --query_cov 0.8 --strand 'both' --maxaccepts 1 --maxrejects 32 --db $ref --threads 16 --blast6out $output ``` With the expectation...
In vsearch 2.6.2, with `--fastq_mergepairs`, failed merges are ventilated as such: ``` Pairs that failed merging due to various reasons: 124844 too few kmers found on same diagonal 19691 potential...