VSEARCH 2.30.0

Author: torognes

README.md

@@ -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/v2.29.4/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/v2.30.0/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
 
@@ -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/v2.29.4.tar.gz
-tar xzf v2.29.4.tar.gz
-cd vsearch-2.29.4
+wget https://github.com/torognes/vsearch/archive/v2.30.0.tar.gz
+tar xzf v2.30.0.tar.gz
+cd vsearch-2.30.0
 ./autogen.sh
 ./configure CFLAGS="-O2" CXXFLAGS="-O2"
 make ARFLAGS="cr"
@@ -91,7 +91,7 @@ wget https://github.com/torognes/vsearch/releases/download/v{VERSION}/vsearch-{V
 tar xzf vsearch-{VERSION}-{OS}-{ARCH}.tar.gz
 ```
 
-Replace `{VERSION}` with the VSEARCH version number (e.g. `2.29.4`), `{OS}` with the target operating system (`linux` or `macos`), and `{ARCH}` with the architecture (`x86_64`, `aarch64`, `ppc64le`, `riscv64`, or `mips64el`). You could add `-static` after `{ARCH}` to get a statically compiled version for Linux (except x86_64). The name of the binary for the RHEL 7 and CentOS 7 Linux distributions ends in `-ubi7`.
+Replace `{VERSION}` with the VSEARCH version number (e.g. `2.30.0`), `{OS}` with the target operating system (`linux` or `macos`), and `{ARCH}` with the architecture (`x86_64`, `aarch64`, `ppc64le`, `riscv64`, or `mips64el`). You could add `-static` after `{ARCH}` to get a statically compiled version for Linux (except x86_64). The name of the binary for the RHEL 7 and CentOS 7 Linux distributions ends in `-ubi7`.
 
 Or, if you are using Windows, download and extract (unzip) the contents of this file:
 
@@ -115,7 +115,7 @@ 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/v2.29.4/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 `$MANPATH`. The manual in both formats is also available with the binary distribution. The manual in PDF form ([vsearch_manual.pdf](https://github.com/torognes/vsearch/releases/download/v2.29.4/vsearch_manual.pdf)) is also attached to the latest [release](https://github.com/torognes/vsearch/releases).
+**Documentation:** The VSEARCH user's manual is available in the `man` folder in the form of a [man page](https://github.com/torognes/vsearch/blob/master/man/vsearch.1). A pdf version ([vsearch_manual.pdf](https://github.com/torognes/vsearch/releases/download/v2.30.0/vsearch_manual.pdf)) will be generated by `make`. To install the manpage manually, copy the `vsearch.1` file or a create a symbolic link to `vsearch.1` in a folder included in your `$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/v2.30.0/vsearch_manual.pdf)) is also attached to the latest [release](https://github.com/torognes/vsearch/releases).
 
 
 ## Packages, plugins, and wrappers

configure.ac

@@ -2,7 +2,7 @@
 # Process this file with autoconf to produce a configure script.
 
 AC_PREREQ([2.63])
-AC_INIT([vsearch], [2.29.4], [torognes@ifi.uio.no], [vsearch], [https://github.com/torognes/vsearch])
+AC_INIT([vsearch], [2.30.0], [torognes@ifi.uio.no], [vsearch], [https://github.com/torognes/vsearch])
 AC_CANONICAL_TARGET
 AM_INIT_AUTOMAKE([subdir-objects])
 AC_LANG([C++])

man/vsearch.1

@@ -1,7 +1,7 @@
 .\" import www macros (URL, TAG, MTO)
 .mso www.tmac
 .\" ============================================================================
-.TH vsearch 1 "February 14, 2025" "version 2.29.4" "USER COMMANDS"
+.TH vsearch 1 "February 27, 2025" "version 2.30.0" "USER COMMANDS"
 .\" ============================================================================
 .SH NAME
 vsearch \(em a versatile open-source tool for microbiome analysis,
@@ -5031,6 +5031,19 @@ Adjust the window size used for chimera detection down from 64 to
 2.23.0, leading to somewhat fewer chimeras being predicted.
 In addition, a compiler pragma has been included in align_simd.cc to
 further protect the compiler from generating wrong code.
+.TP
+.BR v2.30.0\~ "released February 27th, 2025"
+Add options `\-\-n_mismatch`, `\-\-fastq_minqual`, and
+`\-\-fastq_truncee_rate`.  The `\-\-n_mismatch` option will count N's
+as mismatches in alignments, which may be useful to get sensible
+alignments for sequences with lots of N's. By default N's are counted
+as matches. Both the scoring and the counting of matches are
+affected. The new `\-\-fastq_minqual` option for the `fastq_filter`
+and `fastx_filter` commands will discard sequences with any bases with
+a quality scores below the given value. The new
+`\-\-fastq_truncee_rate` option for the same commands will truncate
+sequences at the first position where the number of expected errors
+per base is below the given value.
 .\" ============================================================================
 .\" TODO:
 .\"