[](https://app.travis-ci.com/torognes/vsearch)
# VSEARCH
## Introduction
The aim of this project is to create an alternative to the [USEARCH](https://www.drive5.com/usearch/) tool developed by Robert C. Edgar (2010). The new tool should:
* have open source code with an appropriate open source license
* be free of charge, gratis
* have a 64-bit design that handles very large databases and much more than 4GB of memory
* be as accurate or more accurate than usearch
* be as fast or faster than usearch
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](https://github.com/torognes/vsearch/releases/latest) 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).
| CPU \ OS | GNU/Linux | MacOS | Windows |
| ------------- | :-----------: | :----: | :-------: |
| x86_64 | ✔ | ✔ | ✔ |
| ARMv8 | ✔ | ✔ | |
| POWER8 | ✔ | | |
Various packages, plugins and wrappers are also available from other sources - see [below](https://github.com/torognes/vsearch#packages-plugins-and-wrappers).
The source code compiles correctly with `gcc` (versions 4.8.5 to 12.0)
and `llvm-clang` (3.8 to 15.0). The source code should also compile on
[FreeBSD](https://www.freebsd.org/) and
[NetBSD](https://www.netbsd.org/) systems.
VSEARCH can directly read input query and database files that are compressed using gzip and bzip2 (.gz and .bz2) if the zlib and bzip2 libraries are available.
Most of the nucleotide based commands and options in USEARCH version 7 are supported, as well as some in version 8. The same option names as in USEARCH version 7 has been used in order to make VSEARCH an almost drop-in replacement. VSEARCH does not support amino acid sequences or local alignments. These features may be added in the future.
## Getting Help
If you can't find an answer in the [VSEARCH documentation](https://github.com/torognes/vsearch/releases/download/v2.23.0/vsearch_manual.pdf), please visit the [VSEARCH Web Forum](https://groups.google.com/forum/#!forum/vsearch-forum) to post a question or start a discussion.
## Example
In the example below, VSEARCH will identify sequences in the file database.fsa that are at least 90% identical on the plus strand to the query sequences in the file queries.fsa and write the results to the file alnout.txt.
`./vsearch --usearch_global queries.fsa --db database.fsa --id 0.9 --alnout alnout.txt`
## Download and install
**Source distribution** To download the source distribution from a [release](https://github.com/torognes/vsearch/releases) and build the executable and the documentation, use the following commands:
```
wget https://github.com/torognes/vsearch/archive/v2.23.0.tar.gz
tar xzf v2.23.0.tar.gz
cd vsearch-2.23.0
./autogen.sh
./configure CFLAGS="-O3" CXXFLAGS="-O3"
make
make install # as root or sudo make install
```
You may customize the installation directory using the `--prefix=DIR` option to `configure`. If the compression libraries [zlib](https://www.zlib.net) and/or [bzip2](https://www.sourceware.org/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 were compiled using the C++ cross-compiler. The Windows binary was built using [Mingw-w64](http://mingw-w64.org/).
**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.
```
git clone https://github.com/torognes/vsearch.git
cd vsearch
./autogen.sh
./configure CFLAGS="-O3" CXXFLAGS="-O3"
make
make install # as root or sudo make install
```
**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](https://github.com/torognes/vsearch/releases). 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.
Download the appropriate executable for your system using the following commands if you are using a Linux x86_64 system:
```sh
wget https://github.com/torognes/vsearch/releases/download/v2.23.0/vsearch-2.23.0-linux-x86_64.tar.gz
tar xzf vsearch-2.23.0-linux-x86_64.tar.gz
```
Or these commands if you are using a Linux ppc64le system:
```sh
wget https://github.com/torognes/vsearch/releases/download/v2.23.0/vsearch-2.23.0-linux-ppc64le.tar.gz
tar xzf vsearch-2.23.0-linux-ppc64le.tar.gz
```
Or these commands if you are using a Linux aarch64 (arm64) system:
```sh
wget https://github.com/torognes/vsearch/releases/download/v2.23.0/vsearch-2.23.0-linux-aarch64.tar.gz
tar xzf vsearch-2.23.0-linux-aarch64.tar.gz
```
Or these commands if you are using a Mac with an Apple Silicon CPU:
```sh
wget https://github.com/torognes/vsearch/releases/download/v2.23.0/vsearch-2.23.0-macos-aarch64.tar.gz
tar xzf vsearch-2.23.0-macos-aarch64.tar.gz
```
Or these commands if you are using a Mac with an Intel CPU:
```sh
wget https://github.com/torognes/vsearch/releases/download/v2.23.0/vsearch-2.23.0-macos-x86_64.tar.gz
tar xzf vsearch-2.23.0-macos-x86_64.tar.gz
```
Or if you are using Windows, download and extract (unzip) the contents of this file:
```
https://github.com/torognes/vsearch/releases/download/v2.23.0/vsearch-2.23.0-win-x86_64.zip
```
Linux and Mac: You will now have the binary distribution in a folder called `vsearch-2.23.0-linux-x86_64` or `vsearch-2.23.0-macos-x8
