vsearch | Versatile open-source tool for microbiome analysis | Genomics library

by torognes C++ Version: v2.22.1 License: Non-SPDX

X-Ray Key Features Code Snippets Community Discussions(6)Vulnerabilities Install Support

kandi X-RAY | vsearch Summary

vsearch is a C++ library typically used in Artificial Intelligence, Genomics applications. vsearch has no bugs, it has no vulnerabilities and it has low support. However vsearch has a Non-SPDX License. You can download it from GitHub.

The aim of this project is to create an alternative to the USEARCH tool developed by Robert C. Edgar (2010). The new tool should:. We have implemented a tool called VSEARCH which supports de novo and reference based chimera detection, clustering, full-length and prefix dereplication, rereplication, 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, conversion and merging of paired-end reads. 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. VSEARCH binaries are provided for GNU/Linux on three 64-bit processor architectures: x86-64, POWER8 (ppc64le) and ARMv8 (aarch64). Binaries are also provided for MacOS (version 10.9 Mavericks or later) on Intel (x86-64) and Apple Silicon (ARMv8), as well as Windows (64-bit, version 7 or higher, on x86_64). VSEARCH contains dedicated SIMD code for the three processor architectures (SSE2/SSSE3, AltiVec/VMX/VSX, Neon).

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Support

vsearch has a low active ecosystem.

It has 550 star(s) with 116 fork(s). There are 42 watchers for this library.

It had no major release in the last 12 months.

There are 44 open issues and 434 have been closed. On average issues are closed in 210 days. There are no pull requests.

It has a neutral sentiment in the developer community.

The latest version of vsearch is v2.22.1

Quality

vsearch has 0 bugs and 0 code smells.

Security

vsearch has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.

vsearch code analysis shows 0 unresolved vulnerabilities.

There are 0 security hotspots that need review.

License

vsearch has a Non-SPDX License.

Non-SPDX licenses can be open source with a non SPDX compliant license, or non open source licenses, and you need to review them closely before use.

Reuse

vsearch releases are available to install and integrate.

Installation instructions, examples and code snippets are available.

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vsearch Key Features

No Key Features are available at this moment for vsearch.

vsearch Examples and Code Snippets

No Code Snippets are available at this moment for vsearch.

Community Discussions

Trending Discussions on vsearch

Scraping window.location.href links

mysql.connector.errors.ProgrammingError: Cursor is not connected

Snakemake tries to run rule, reason: Missing output files, but files are temporary

Problem on describing table through SQL Query (SQL x Python)

Batch file change a drive letter string in a log file

Module gets imported under a syntactically false name space?

QUESTION

Scraping window.location.href links

Asked 2021-Sep-17 at 06:15

How do I print out links that contain ftype2?

I'm fairly new to bs4,from what I've been reading, the findAll or find_all method is only used for tags. It can't be used for windows.location.href kind of tags.

It might seem that regex is the last option, but I'm not sure how that will work since I can't figure out how to select those particular links because the select tag in bs4 doesn't work with Window.location.href

...

ANSWER

Answered 2021-Sep-17 at 06:15

As far as I understand, you are looking for a elements whose href contains the text ftype=2. Below is the code you can use to do so:

Source https://stackoverflow.com/questions/69217844

QUESTION

mysql.connector.errors.ProgrammingError: Cursor is not connected

Asked 2020-Sep-20 at 15:26

after writing word on entry page that i want to search and letters inside of word it goes to /search4 and i get error on page with mysql.connector.errors.ProgrammingError: Cursor is not connected after checking here is code.

...

ANSWER

Answered 2020-Sep-20 at 15:26

The cursor.execute call should be inside the with block, because cursor only exists within that block.

It's literally a missing indentation:

Source https://stackoverflow.com/questions/63980548

QUESTION

Snakemake tries to run rule, reason: Missing output files, but files are temporary

Asked 2020-Jul-17 at 08:40

I have a series of rule leading into using vsearch, with the barebones shown here:

...

ANSWER

Answered 2020-Jul-17 at 08:40

I would move seqkit fq2fa to its own rule producing the temp file nedded by vsearch. Like (not tested):

Source https://stackoverflow.com/questions/62942329

QUESTION

Problem on describing table through SQL Query (SQL x Python)

Asked 2020-Jun-23 at 03:18

I'm following a book and right now the objective is to write some Python code to interact with log table. So far, I have successfully defined the connection characteristics for the database, imported the driver module, created a connection object, and created a cursor. (By the way, I'm using IDLE)

...

ANSWER

Answered 2020-Jun-23 at 03:18

It seems that you have a typo in your statement. Change the spelling mistake.

Source https://stackoverflow.com/questions/62526443

QUESTION

Batch file change a drive letter string in a log file

Asked 2020-May-07 at 20:55

trying to replace drive designation inside Idrive log files using a batch. Amateur programmer trying to understand batch files for years but still don't get advanced techniques. I suspect the '\' backslash needs to be escaped but nothing I try works.

Sample Log input:

...

ANSWER

Answered 2020-May-07 at 19:14

Your code works fine for me - when I correct just one line:

Source https://stackoverflow.com/questions/61665022

QUESTION

Module gets imported under a syntactically false name space?

Asked 2020-Mar-25 at 14:46

I am following along with the O'Riley Head First Python (2nd Edition) Course. At one point you will create a webapp and deploy it to pythonanywhere (chapter5).

The webapp uses two functions, imported from a module, created earlier.

The module is called vsearch.py. I also created a readme.txt and a setup.py and used setuptools to create a source distribution file using :

python3 setup.py sdist

The code of the setup.py read as follows:

...

ANSWER

Answered 2020-Mar-25 at 14:46

pip install --user (with emphasized --user) installed the package into your user directory: /home/Mohr/.local/lib/pythonX.Y/site-packages/.

To run your WSGI application you probably use a virtual environment in which the user-installed modules are not available. To use modules in the venv you have to install everything in the venv. So activate the venv in a terminal and install the module with the venv's pip:

Source https://stackoverflow.com/questions/60835233

Community Discussions, Code Snippets contain sources that include Stack Exchange Network

Vulnerabilities

No vulnerabilities reported

Install vsearch

Source distribution To download the source distribution from a release and build the executable and the documentation, use the following commands:. You may customize the installation directory using the --prefix=DIR option to configure. If the compression libraries zlib and/or bzip2 are installed on the system, they will be detected automatically and support for compressed files will be included in vsearch. Support for compressed files may be disabled using the --disable-zlib and --disable-bzip2 options to configure. A PDF version of the manual will be created from the vsearch.1 manual file if ps2pdf is available, unless disabled using the --disable-pdfman option to configure. It is recommended to run configure with the options CFLAGS="-O3" and CXXFLAGS="-O3". Other options may also be applied to configure, please run configure -h to see them all. GNU autoconf (version 2.63 or later), automake and the GCC C++ compiler is required to build vsearch. Version 3.82 or later of Make may be required on Linux, while version 3.81 is sufficient on macOS. The distributed Linux ppc64le and aarch64 binaries and the Windows binary were compiled using the Mingw-w64 C++ cross-compiler. Cloning the repo Instead of downloading the source distribution as a compressed archive, you could clone the repo and build it as shown below. The options to configure as described above are still valid. Binary distribution Starting with version 1.4.0, binary distribution files containing pre-compiled binaries as well as the documentation will be made available as part of each release. The included executables include support for input files compressed by zlib and bzip2 (with files usually ending in .gz or .bz2). Binary distributions are provided for x86-64 systems running GNU/Linux, macOS (version 10.7 or higher) or Windows (64-bit, version 7 or higher), 64-bit AMDv8 (aarch64) systems running GNU/Linux or macOS, as well as POWER8 (ppc64le) systems running GNU/Linux.