New upstream version 2.13.5 (59e4ea33) · Commits · Debian Med / vsearch

README.md

+39 −23

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		@@ -16,7 +16,17 @@ We have implemented a tool called VSEARCH which supports de novo and reference

		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 x86-64 systems running GNU/Linux, macOS (version 10.7 or higher) and Windows (64-bit, version 7 or higher), as well as for 64-bit little-endian POWER8 (ppc64le) and 64-bit ARMv8 systems (aarch64) running GNU/Linux. VSEARCH contains dedicated SIMD code for these three processors architectures (SSE2, AltiVec/VMX/VSX, Neon).
		[VSEARCH binaries](https://github.com/torognes/vsearch/releases/latest) are provided for GNU/Linux on three processor architectures: x86-64, 64-bit little-endian POWER8 (ppc64le) and 64-bit ARMv8 (aarch64). VSEARCH contains dedicated SIMD code for these three processors architectures (SSE2/SSSE3, AltiVec/VMX/VSX, Neon). Binaries are also provided for MacOS (version 10.9 Mavericks or later) and Windows (64-bit, version 7 or higher).

		\| 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 to 9.1) and llvm-clang (3.8 to 9.0). 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.

		@@ -24,7 +34,7 @@ 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/v2.10.4/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/v2.13.5/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

		@@ -37,9 +47,9 @@ 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/v2.10.4.tar.gz
		tar xzf v2.10.4.tar.gz
		cd vsearch-2.10.4
		wget https://github.com/torognes/vsearch/archive/v2.13.5.tar.gz
		tar xzf v2.13.5.tar.gz
		cd vsearch-2.13.5
		./autogen.sh
		./configure
		make
		@@ -68,57 +78,61 @@ 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/v2.10.4/vsearch-2.10.4-linux-x86_64.tar.gz
		tar xzf vsearch-2.10.4-linux-x86_64.tar.gz
		wget https://github.com/torognes/vsearch/releases/download/v2.13.5/vsearch-2.13.5-linux-x86_64.tar.gz
		tar xzf vsearch-2.13.5-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/v2.10.4/vsearch-2.10.4-linux-ppc64le.tar.gz
		tar xzf vsearch-2.10.4-linux-ppc64le.tar.gz
		wget https://github.com/torognes/vsearch/releases/download/v2.13.5/vsearch-2.13.5-linux-ppc64le.tar.gz
		tar xzf vsearch-2.13.5-linux-ppc64le.tar.gz
		```

		Or these commands if you are using a Linux aarch64 system:

		```sh
		wget https://github.com/torognes/vsearch/releases/download/v2.10.4/vsearch-2.10.4-linux-aarch64.tar.gz
		tar xzf vsearch-2.10.4-linux-aarch64.tar.gz
		wget https://github.com/torognes/vsearch/releases/download/v2.13.5/vsearch-2.13.5-linux-aarch64.tar.gz
		tar xzf vsearch-2.13.5-linux-aarch64.tar.gz
		```

		Or these commands if you are using a Mac:

		```sh
		wget https://github.com/torognes/vsearch/releases/download/v2.10.4/vsearch-2.10.4-macos-x86_64.tar.gz
		tar xzf vsearch-2.10.4-macos-x86_64.tar.gz
		wget https://github.com/torognes/vsearch/releases/download/v2.13.5/vsearch-2.13.5-macos-x86_64.tar.gz
		tar xzf vsearch-2.13.5-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/v2.10.4/vsearch-2.10.4-win-x86_64.zip
		https://github.com/torognes/vsearch/releases/download/v2.13.5/vsearch-2.13.5-win-x86_64.zip
		```

		Linux and Mac: You will now have the binary distribution in a folder called `vsearch-2.10.4-linux-x86_64` or `vsearch-2.10.4-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`.
		Linux and Mac: You will now have the binary distribution in a folder called `vsearch-2.13.5-linux-x86_64` or `vsearch-2.13.5-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`.

		Windows: You will now have the binary distribution in a folder called `vsearch-2.10.4-win-x86_64`. The vsearch executable is called `vsearch.exe`. The manual in PDF format is called `vsearch_manual.pdf`.
		Windows: You will now have the binary distribution in a folder called `vsearch-2.13.5-win-x86_64`. The vsearch executable is called `vsearch.exe`. The manual in PDF format is called `vsearch_manual.pdf`.


		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/v2.10.4/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 `$MANPATH`. The manual in both formats is also available with the binary distribution. The manual in PDF form ([vsearch_manual.pdf](https://github.com/torognes/vsearch/releases/download/v2.10.4/vsearch_manual.pdf)) is also attached to the latest [release](https://github.com/torognes/vsearch/releases).
		Documentation The VSEARCH user's manual is available in the `man` folder in the form of a [man page](https://github.com/torognes/vsearch/blob/master/man/vsearch.1). A pdf version ([vsearch_manual.pdf](https://github.com/torognes/vsearch/releases/download/v2.13.5/vsearch_manual.pdf)) will be generated by `make`. To install the manpage manually, copy the `vsearch.1` file or a create a symbolic link to `vsearch.1` in a folder included in your `$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/v2.13.5/vsearch_manual.pdf)) is also attached to the latest [release](https://github.com/torognes/vsearch/releases).


		## Plugins, packages, and wrappers

		QIIME 2 plugin Thanks to the [QIIME 2](https://github.com/qiime2) team, there is now a plugin called [q2-vsearch](https://github.com/qiime2/q2-vsearch) for [QIIME 2](https://qiime2.org).
		## Packages, plugins, and wrappers

		Conda package Thanks to the [BioConda](https://bioconda.github.io/) team, there is now a [vsearch package](https://anaconda.org/bioconda/vsearch) in [Conda](https://conda.io/).

		Homebrew package Thanks to [Torsten Seeman](https://github.com/tseemann), a [vsearch package](https://github.com/Homebrew/homebrew-science/pull/2409) for [Homebrew](http://brew.sh/) has been made.

		Debian package Thanks to the [Debian Med](https://www.debian.org/devel/debian-med/) team, there is now a [vsearch](https://packages.debian.org/sid/vsearch) package in [Debian](https://www.debian.org/).

		FreeBSD ports package Thanks to [Jason Bacon](https://github.com/outpaddling), a [vsearch](https://www.freebsd.org/cgi/ports.cgi?query=vsearch&stype=all) [FreeBSD ports](https://www.freebsd.org/ports/) package is available. Install the binary package with `pkg install vsearch`, or build from source with additional optimizations.

		Galaxy wrapper Thanks to the work of the [Intergalactic Utilities Commission](https://wiki.galaxyproject.org/IUC) members, vsearch is now part of the [Galaxy ToolShed](https://toolshed.g2.bx.psu.edu/view/iuc/vsearch/).

		Homebrew package Thanks to [Torsten Seeman](https://github.com/tseemann), a [vsearch package](https://github.com/Homebrew/homebrew-science/pull/2409) for [Homebrew](http://brew.sh/) has been made.

		Pkgsrc package Thanks to [Jason Bacon](https://github.com/outpaddling), a vsearch [pkgsrc](https://www.pkgsrc.org) package is available for NetBSD and other UNIX-like systems. Install the binary package with `pkgin install vsearch`, or build from source with additional optimizations.

		QIIME 2 plugin Thanks to the [QIIME 2](https://github.com/qiime2) team, there is now a plugin called [q2-vsearch](https://github.com/qiime2/q2-vsearch) for [QIIME 2](https://qiime2.org).


		## Converting output to a biom file for use in QIIME and other software

		@@ -176,11 +190,11 @@ The code is written in C++ but most of it is actually mostly C with some C++ syn

		File \| Description
		---\|---
		abundance.cc \| Code for extracting and printing abundance information from FASTA headers
		align.cc \| New Needleman-Wunsch global alignment, serial. Only for testing.
		align_simd.cc \| SIMD parallel global alignment of 1 query with 8 database sequences
		allpairs.cc \| All-vs-all optimal global pairwise alignment (no heuristics)
		arch.cc \| Architecture specific code (Mac/Linux)
		attributes.cc \| Extraction and printing of attributes in FASTA headers
		bitmap.cc \| Implementation of bitmaps
		chimera.cc \| Chimera detection
		city.cc \| CityHash code
		@@ -197,6 +211,8 @@ File \| Description
		fastqjoin.cc \| FASTQ paired-end reads joining
		fastqops.cc \| FASTQ file statistics etc
		fastx.cc \| Detection of FASTA and FASTQ files, wrapper for FASTA and FASTQ parsers
		filter.cc \| Trimming and filtering of sequences in FASTA and FASTQ files
		getseq.cc \| Extraction of sequences based on header labels
		kmerhash.cc \| Hash for kmers used by paired-end read merger
		linmemalign.cc \| Linear memory global sequence aligner
		maps.cc \| Various character mapping arrays

configure.ac

+2 −2

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		@@ -2,7 +2,7 @@
		# Process this file with autoconf to produce a configure script.

		AC_PREREQ([2.63])
		AC_INIT([vsearch], [2.10.4], [torognes@ifi.uio.no])
		AC_INIT([vsearch], [2.13.5], [torognes@ifi.uio.no])
		AC_CANONICAL_TARGET
		AM_INIT_AUTOMAKE([subdir-objects])
		AC_LANG([C++])
		@@ -10,7 +10,7 @@ AC_CONFIG_SRCDIR([src/vsearch.cc])
		AC_CONFIG_HEADERS([config.h])

		AC_SUBST(MACOSX_DEPLOYMENT_TARGET)
		MACOSX_DEPLOYMENT_TARGET="10.7"
		MACOSX_DEPLOYMENT_TARGET="10.9"

		# Set default gcc and g++ options

man/vsearch.1

+425 −90

File changed.

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src/Makefile.am

+9 −3

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		@@ -12,20 +12,21 @@ endif

		AM_CFLAGS=$(AM_CXXFLAGS)

		export MACOSX_DEPLOYMENT_TARGET
		export MACOSX_DEPLOYMENT_TARGET=10.9

		VSEARCHHEADERS=\
		abundance.h \
		align.h \
		align_simd.h \
		allpairs.h \
		arch.h \
		attributes.h \
		bitmap.h \
		chimera.h \
		city.h \
		citycrc.h \
		cluster.h \
		cpu.h \
		cut.h \
		db.h \
		dbhash.h \
		dbindex.h \
		@@ -37,6 +38,8 @@ fastq.h \
		fastqjoin.h \
		fastqops.h \
		fastx.h \
		filter.h \
		getseq.h \
		kmerhash.h \
		linmemalign.h \
		maps.h \
		@@ -107,14 +110,15 @@ endif
		endif

		__top_builddir__bin_vsearch_SOURCES = $(VSEARCHHEADERS) \
		abundance.cc \
		align.cc \
		align_simd.cc \
		allpairs.cc \
		arch.cc \
		attributes.cc \
		bitmap.cc \
		chimera.cc \
		cluster.cc \
		cut.cc \
		db.cc \
		dbhash.cc \
		dbindex.cc \
		@@ -126,6 +130,8 @@ fastq.cc \
		fastqjoin.cc \
		fastqops.cc \
		fastx.cc \
		filter.cc \
		getseq.cc \
		kmerhash.cc \
		linmemalign.cc \
		maps.cc \

src/align.cc

+2 −10

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		@@ -2,7 +2,7 @@

		VSEARCH: a versatile open source tool for metagenomics

		Copyright (C) 2014-2018, Torbjorn Rognes, Frederic Mahe and Tomas Flouri
		Copyright (C) 2014-2019, Torbjorn Rognes, Frederic Mahe and Tomas Flouri
		All rights reserved.

		Contact: Torbjorn Rognes <torognes@ifi.uio.no>,
		@@ -169,14 +169,6 @@ void nw_exit(struct nwinfo_s * nw)
		xfree(nw);
		}

		inline int nt_identical(char a, char b)
		{
		if (chrmap_4bit[(int)a] == chrmap_4bit[(int)b])
		return 1;
		else
		return 0;
		}

		inline int64_t getscore(int64_t * score_matrix, char a, char b)
		{
		return score_matrix[(chrmap_4bit[(int)a]<<4) + chrmap_4bit[(int)b]];
		@@ -394,7 +386,7 @@ void nw_align(char * dseq,
		else
		{
		score += getscore(score_matrix, dseq[j-1], qseq[i-1]);
		if (nt_identical(dseq[j-1], qseq[i-1]))
		if (chrmap_4bit[(int)(dseq[j-1])] & chrmap_4bit[(int)(qseq[i-1])])
		matches++;
		i--;
		j--;