Difference between revisions of "VSearch"
(Created page with "Category:SoftwareCategory:BiologyCategory:NGS {|<!--CONFIGURATION: REQUIRED--> |{{#vardefine:app|vsearch}} |{{#vardefine:url|https://github.com/torognes/vsearch}}...") |
Moskalenko (talk | contribs) m (Text replacement - "#uppercase" to "uc") |
||
| Line 37: | Line 37: | ||
--> | --> | ||
==System Variables== | ==System Variables== | ||
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory |
<!--Configuration--> | <!--Configuration--> | ||
{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
Revision as of 21:29, 6 December 2019
Description
We have implemented a tool called VSEARCH which supports de novo and reference based chimera detection, clustering, full-length and prefix dereplication, reverse complementation, masking, all-vs-all pairwise global alignment, exact and global alignment searching, shuffling, subsampling and sorting. It also supports FASTQ file analysis, filtering and conversion.
VSEARCH stands for vectorized search, as the tool takes advantage of parallelism in the form of SIMD vectorization as well as multiple threads to perform accurate alignments at high speed. VSEARCH uses an optimal global aligner (full dynamic programming Needleman-Wunsch), in contrast to USEARCH which by default uses a heuristic seed and extend aligner. This usually results in more accurate alignments and overall improved sensitivity (recall) with VSEARCH, especially for alignments with gaps.
Required Modules
Serial
- vsearch
System Variables
- HPC_VSEARCH_DIR - installation directory
Citation
If you publish research that uses vsearch you have to cite it as follows:
No papers about VSEARCH have been published yet, but a manuscript is in preparation. For now, please cite the VSEARCH GitHub repository. Release 1.4.0 has doi 10.5281/zenodo.31443.