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VSEARCH 2.29.0
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torognes committed Sep 26, 2024
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38 changes: 19 additions & 19 deletions README.md
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Expand Up @@ -39,7 +39,7 @@ Most of the nucleotide based commands and options in USEARCH version 7 are suppo

## Getting Help

If you can't find an answer in the [VSEARCH documentation](https://github.com/torognes/vsearch/releases/download/v2.28.1/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.
If you can't find an answer in the [VSEARCH documentation](https://github.com/torognes/vsearch/releases/download/v2.29.0/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

Expand All @@ -52,9 +52,9 @@ In the example below, VSEARCH will identify sequences in the file database.fsa t
**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/v2.28.1.tar.gz
tar xzf v2.28.1.tar.gz
cd vsearch-2.28.1
wget https://github.com/torognes/vsearch/archive/v2.29.0.tar.gz
tar xzf v2.29.0.tar.gz
cd vsearch-2.29.0
./autogen.sh
./configure CFLAGS="-O3" CXXFLAGS="-O3"
make ARFLAGS="cr"
Expand Down Expand Up @@ -83,48 +83,48 @@ Binary distributions are provided for x86-64 systems running GNU/Linux, macOS (v
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/v2.28.1/vsearch-2.28.1-linux-x86_64.tar.gz
tar xzf vsearch-2.28.1-linux-x86_64.tar.gz
wget https://github.com/torognes/vsearch/releases/download/v2.29.0/vsearch-2.29.0-linux-x86_64.tar.gz
tar xzf vsearch-2.29.0-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/v2.28.1/vsearch-2.28.1-linux-ppc64le.tar.gz
tar xzf vsearch-2.28.1-linux-ppc64le.tar.gz
wget https://github.com/torognes/vsearch/releases/download/v2.29.0/vsearch-2.29.0-linux-ppc64le.tar.gz
tar xzf vsearch-2.29.0-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/v2.28.1/vsearch-2.28.1-linux-aarch64.tar.gz
tar xzf vsearch-2.28.1-linux-aarch64.tar.gz
wget https://github.com/torognes/vsearch/releases/download/v2.29.0/vsearch-2.29.0-linux-aarch64.tar.gz
tar xzf vsearch-2.29.0-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/v2.28.1/vsearch-2.28.1-macos-aarch64.tar.gz
tar xzf vsearch-2.28.1-macos-aarch64.tar.gz
wget https://github.com/torognes/vsearch/releases/download/v2.29.0/vsearch-2.29.0-macos-aarch64.tar.gz
tar xzf vsearch-2.29.0-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/v2.28.1/vsearch-2.28.1-macos-x86_64.tar.gz
tar xzf vsearch-2.28.1-macos-x86_64.tar.gz
wget https://github.com/torognes/vsearch/releases/download/v2.29.0/vsearch-2.29.0-macos-x86_64.tar.gz
tar xzf vsearch-2.29.0-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/v2.28.1/vsearch-2.28.1-win-x86_64.zip
https://github.com/torognes/vsearch/releases/download/v2.29.0/vsearch-2.29.0-win-x86_64.zip
```

Linux and Mac: You will now have the binary distribution in a folder called `vsearch-2.28.1-linux-x86_64` or `vsearch-2.28.1-macos-x86_64` in which you will find three subfolders `bin`, `man` and `doc`. We recommend making a copy or a symbolic link to the vsearch binary `bin/vsearch` in a folder included in your `$PATH`, and a copy or a symbolic link to the vsearch man page `man/vsearch.1` in a folder included in your `$MANPATH`. The PDF version of the manual is available in `doc/vsearch_manual.pdf`. Versions with statically compiled libraries are available for Linux systems. These have "-static" in their name, and could be used on systems that do not have all the necessary libraries installed.
Linux and Mac: You will now have the binary distribution in a folder called `vsearch-2.29.0-linux-x86_64` or `vsearch-2.29.0-macos-x86_64` in which you will find three subfolders `bin`, `man` and `doc`. We recommend making a copy or a symbolic link to the vsearch binary `bin/vsearch` in a folder included in your `$PATH`, and a copy or a symbolic link to the vsearch man page `man/vsearch.1` in a folder included in your `$MANPATH`. The PDF version of the manual is available in `doc/vsearch_manual.pdf`. Versions with statically compiled libraries are available for Linux systems. These have "-static" in their name, and could be used on systems that do not have all the necessary libraries installed.

**Windows**: You will now have the binary distribution in a folder
called `vsearch-2.28.1-win-x86_64`. The vsearch executable is called
called `vsearch-2.29.0-win-x86_64`. The vsearch executable is called
`vsearch.exe`. The manual in PDF format is called
`vsearch_manual.pdf`. If you want to be able to call `vsearch.exe`
from any command prompt window, you can put the vsearch executable in
Expand All @@ -137,7 +137,7 @@ and `zlib1.dll` files required for reading compressed input
files. These DLL's have been obtained for mingw-w64 from the MSYS2
platform.

**Documentation** The VSEARCH user's manual is available in the `man` folder in the form of a [man page](https://github.com/torognes/vsearch/blob/master/man/vsearch.1). A pdf version ([vsearch_manual.pdf](https://github.com/torognes/vsearch/releases/download/v2.28.1/vsearch_manual.pdf)) will be generated by `make`. To install the manpage manually, copy the `vsearch.1` file or a create a symbolic link to `vsearch.1` in a folder included in your `$MANPATH`. The manual in both formats is also available with the binary distribution. The manual in PDF form ([vsearch_manual.pdf](https://github.com/torognes/vsearch/releases/download/v2.28.1/vsearch_manual.pdf)) is also attached to the latest [release](https://github.com/torognes/vsearch/releases).
**Documentation** The VSEARCH user's manual is available in the `man` folder in the form of a [man page](https://github.com/torognes/vsearch/blob/master/man/vsearch.1). A pdf version ([vsearch_manual.pdf](https://github.com/torognes/vsearch/releases/download/v2.29.0/vsearch_manual.pdf)) will be generated by `make`. To install the manpage manually, copy the `vsearch.1` file or a create a symbolic link to `vsearch.1` in a folder included in your `$MANPATH`. The manual in both formats is also available with the binary distribution. The manual in PDF form ([vsearch_manual.pdf](https://github.com/torognes/vsearch/releases/download/v2.29.0/vsearch_manual.pdf)) is also attached to the latest [release](https://github.com/torognes/vsearch/releases).


## Packages, plugins, and wrappers
Expand Down Expand Up @@ -181,7 +181,7 @@ Compiling VSEARCH requires either GCC (`g++`) or `clang`, `make` and the autotoo

VSEARCH will automatically check whether these libraries are available and load them dynamically.

On Windows these libraries are called `zlib1.dll` and `libbz2.dll`. These DLL's are included with the released distribution of vsearch 2.28.1 and later.
On Windows these libraries are called `zlib1.dll` and `libbz2.dll`. These DLL's are included with the released distribution of vsearch 2.29.0 and later.

To create the PDF file with the manual the ps2pdf tool is required. It is part of the `ghostscript` package.

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2 changes: 1 addition & 1 deletion configure.ac
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Expand Up @@ -2,7 +2,7 @@
# Process this file with autoconf to produce a configure script.

AC_PREREQ([2.63])
AC_INIT([vsearch], [2.28.1], [[email protected]], [vsearch], [https://github.com/torognes/vsearch])
AC_INIT([vsearch], [2.29.0], [[email protected]], [vsearch], [https://github.com/torognes/vsearch])
AC_CANONICAL_TARGET
AM_INIT_AUTOMAKE([subdir-objects])
AC_LANG([C++])
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76 changes: 65 additions & 11 deletions man/vsearch.1
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@@ -1,7 +1,7 @@
.\" import www macros (URL, TAG, MTO)
.mso www.tmac
.\" ============================================================================
.TH vsearch 1 "April 26, 2024" "version 2.28.1" "USER COMMANDS"
.TH vsearch 1 "September 26, 2024" "version 2.29.0" "USER COMMANDS"
.\" ============================================================================
.SH NAME
vsearch \(em a versatile open-source tool for microbiome analysis,
Expand Down Expand Up @@ -210,14 +210,15 @@ Needleman-Wunsch algorithm, making use of the Streaming SIMD
Extensions (SSE2) of post-2003 x86-64 CPUs. If SSE2 instructions are
not available, \fBvsearch\fR exits with an error message. On Power8
CPUs it will use AltiVec/VSX/VMX instructions, and on ARMv8 CPUs it
will use Neon instructions. Memory usage increases rapidly with
sequence length: for example comparing two sequences of length 1 kb
requires 8 MB of memory per thread, and comparing two 10 kb sequences
requires 800 MB of memory per thread. For comparisons involving
sequences with a length product greater than 25 million (for example
two sequences of length 5 kb), \fBvsearch\fR uses a slower alignment
method described by Hirschberg (1975) and Myers and Miller (1988),
with much smaller memory requirements.
will use Neon instructions. On other systems it can use the SIMD
Everywhere (simde) library, if available. Memory usage increases
rapidly with sequence length: for example comparing two sequences of
length 1 kb requires 8 MB of memory per thread, and comparing two 10
kb sequences requires 800 MB of memory per thread. For comparisons
involving sequences with a length product greater than 25 million (for
example two sequences of length 5 kb), \fBvsearch\fR uses a slower
alignment method described by Hirschberg (1975) and Myers and Miller
(1988), with much smaller memory requirements.
.\" ----------------------------------------------------------------------------
.SS Input
\fBvsearch\fR accept as input fasta or fastq files containing one or
Expand Down Expand Up @@ -4098,8 +4099,7 @@ greater than 2:
.\"
.\" ============================================================================
.SH AUTHORS
Implementation by Torbjørn Rognes and Tomás Flouri, documentation by
Frédéric Mahé.
Implementation and documentation by Torbjørn Rognes, Frédéric Mahé and Tomás Flouri.
.PP
.\" ============================================================================
.SH CITATION
Expand Down Expand Up @@ -4934,6 +4934,60 @@ ensure reproducibility of the random choices in the algorithm.
.BR v2.28.1\~ "released April 26th, 2024"
Fix a segmentation fault that could occur with the blast6out and
output_no_hits options.
.TP
.BR v2.29.0\~ "released September 26th, 2024"
This version fixes seven bugs (see changelog below), adds
initial support for RISC-V architectures, and improves code quality
and code testing (1,210 new tests):
.RS
.IP - 2
add: experimental support for RISCV64 and other 64-bit little-endian
architectures, thanks to Michael R. Crusoe and his fellow Debian
developers (issue #566),
.IP -
add: official support for clang-19 and gcc 14,
.IP -
add: beta support for clang-20,
.IP -
remove: unused \-\-output option for command \-\-fastq_stats (issue #572),
.IP -
fix: bug in \-\-sintax when selecting the best lineage (only low
confidence values below 0.5 were affected) (issue #573),
.IP -
fix: out-of-bounds error in \-\-fastq_stats when processing empty
reads (issue #571),
.IP -
fix: bug in \-\-cut, patterns with multiple cutting sites were not
detected (commit 4c4f9fa70f14b28d50185dbf322cf5727087e86a),
.IP -
fix: memory error (segmentation fault) when using \-\-derep_id and
\-\-strand (issue #565),
.IP -
fix: \-\-fastq_join now obeys to \-\-quiet and \-\-log options
(commit 87f968b09f17c17ebf8db00aebe86e89b13a3948),
.IP -
fix: \-\-fastq_join quality padding is now also set to Q40 when
quality offset is 64 (commit be0bf9b48d782286c4ce38f0bf1a4c82bd230250),
.IP -
fix: (partial) \-\-fastq_join's handling of abundance annotations
(commit f2bbcb421dc2f4dfa6603b9f31ec3e4598c1b591),
.IP -
improve: additional safeguards to validate input values and to make
sure that they are within acceptable limits. Changes concern options
\-\-abskew (commit a530dd8990f8a05cb25fc0b6a5da5a14d28fbedd) and
\-\-fastq_maxdiffs (commit 4b254db7f120bfd49e86185ef3cd9070c236f940),
.IP -
improve: code quality (1.3k+ commits, 6k+ clang-tidy warnings eliminated),
.IP -
improve: documentation and help messages (issue #568),
.IP -
improve: complete refactoring and modernization of a subset of
commands (\-\-sortbylength, \-\-sortbysize, \-\-shuffle,
\-\-rereplicate, \-\-cut, \-\-fastq_join, \-\-fasta2fastq,
\-\-fastq_chars),
.IP -
improve: code-coverage of our test-suite for the above-mentioned commands (1,210 new tests, 4,753 in total)
.RE
.LP
.\" ============================================================================
.\" TODO:
Expand Down

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