New upstream version 2.8.0

language:

- cpp

os:

- linux

- osx

compiler:

- g++

- clang

install:

- if [ $TRAVIS_OS_NAME = linux ]; then sudo apt-get install ghostscript; else brew install ghostscript; fi

script:

- ./autogen.sh

- ./configure

- make

[![Build Status](https://travis-ci.org/torognes/vsearch.svg?branch=master)](https://travis-ci.org/torognes/vsearch)

# VSEARCH

## Introduction

## Getting Help

If you can't find an answer in the [VSEARCH documentation](https://github.com/torognes/vsearch/releases/download/v2.7.1/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/v2.8.0/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

**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/v2.7.1.tar.gz

tar xzf v2.7.1.tar.gz

cd vsearch-2.7.1

wget https://github.com/torognes/vsearch/archive/v2.8.0.tar.gz

tar xzf v2.8.0.tar.gz

cd vsearch-2.8.0

./autogen.sh

./configure

make

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/v2.7.1/vsearch-2.7.1-linux-x86_64.tar.gz

tar xzf vsearch-2.7.1-linux-x86_64.tar.gz

wget https://github.com/torognes/vsearch/releases/download/v2.8.0/vsearch-2.8.0-linux-x86_64.tar.gz

tar xzf vsearch-2.8.0-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/v2.7.1/vsearch-2.7.1-linux-ppc64le.tar.gz

tar xzf vsearch-2.7.1-linux-ppc64le.tar.gz

wget https://github.com/torognes/vsearch/releases/download/v2.8.0/vsearch-2.8.0-linux-ppc64le.tar.gz

tar xzf vsearch-2.8.0-linux-ppc64le.tar.gz

```

Or these commands if you are using a Mac:

```sh

wget https://github.com/torognes/vsearch/releases/download/v2.7.1/vsearch-2.7.1-macos-x86_64.tar.gz

tar xzf vsearch-2.7.1-macos-x86_64.tar.gz

wget https://github.com/torognes/vsearch/releases/download/v2.8.0/vsearch-2.8.0-macos-x86_64.tar.gz

tar xzf vsearch-2.8.0-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/v2.7.1/vsearch-2.7.1-win-x86_64.zip

https://github.com/torognes/vsearch/releases/download/v2.8.0/vsearch-2.8.0-win-x86_64.zip

```

Linux and Mac: You will now have the binary distribution in a folder called `vsearch-2.7.1-linux-x86_64` or `vsearch-2.7.1-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`.

Linux and Mac: You will now have the binary distribution in a folder called `vsearch-2.8.0-linux-x86_64` or `vsearch-2.8.0-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`.

Windows: You will now have the binary distribution in a folder called `vsearch-2.7.1-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-2.8.0-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/v2.7.1/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/v2.7.1/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/v2.8.0/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/v2.8.0/vsearch_manual.pdf)) is also attached to the latest [release](https://github.com/torognes/vsearch/releases).

## Plugins, packages, and wrappers

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

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

## VSEARCH license and third party licenses

# Process this file with autoconf to produce a configure script.

AC_PREREQ([2.63])

AC_INIT([vsearch], [2.7.1], [torognes@ifi.uio.no])

AC_INIT([vsearch], [2.8.0], [torognes@ifi.uio.no])

AC_CANONICAL_TARGET

AM_INIT_AUTOMAKE([subdir-objects])

AC_LANG([C++])

.\" ============================================================================

.TH vsearch 1 "February 16, 2018" "version 2.7.1" "USER COMMANDS"

.TH vsearch 1 "April 24, 2018" "version 2.8.0" "USER COMMANDS"

.\" ============================================================================

.SH NAME

vsearch \(em chimera detection, clustering, dereplication and

rereplication, FASTA/FASTQ file processing, masking, pairwise

alignment, searching, shuffling, sorting and subsampling of amplicons

for metagenomics, genomics, and population genetics.

alignment, searching, shuffling, sorting, subsampling, and taxonomic

classification of amplicons for metagenomics, genomics, and population

genetics.

.\" ============================================================================

.SH SYNOPSIS

.\" left justified, ragged right

\-\-sample_size \fIpositive integer\fR) [\fIoptions\fR]

.PP

.RE

Taxonomic classification:

.RS

\fBvsearch\fR \-\-sintax \fIfastafile\fR \-\-db \fIfastafile\fR

\-\-tabbedout \fIoutputfile\fR [\-\-sintax_cutoff \fIreal\fR]

[\fIoptions\fR]

.PP

.RE

UDB database handling:

.RS

\fBvsearch\fR \-\-makeudb_usearch \fIfastafile\fR \-\-output \fIoutputfile\fR [\fIoptions\fR]

has a strong influence on the merging success rate. The default

value is 10.

.TP

.BI \-\-fastq_maxdiffpct\~ real

When using \-\-fastq_mergepairs, specify the maximum percentage of

non-matching nucleotides allowed in the overlap region. The default

value is 100.0%. There are other more sophisticated rules in the

merging algorithm that will discard read pairs with a high fraction of

mismatches.

.TP

.BI \-\-fastq_maxee\~ real

When using \-\-fastq_filter, \-\-fastq_mergepairs or \-\-fastx_filter,

discard sequences with more than the specified number of expected

discarded (no limit by default). Staggered reads are not merged unless

the \-\-fastq_allowmergestagger option is specified. The minimum

length of the overlap region between the reads may be specified with

the \-\-fastq_minovlen option (default 10), and the overlap region may

the \-\-fastq_minovlen option (default 10). The overlap region may

not include more mismatches than specified with the \-\-fastq_maxdiffs

option (10 by default), otherwise the read pair is discarded.

Additional rules will avoid merging of reads that cannot be aligned

reliably and unambiguously. The mimimum and maximum length of the

merged sequence may be specified with the \-\-fastq_minmergelen and

option (10 by default) or a higher percentage of mismatches than

specified with the \-\-fastq_maxdiffpct option (100.0% by default),

otherwise the read pair is discarded. Additional rules will avoid

merging of reads that cannot be aligned reliably and

unambiguously. The mimimum and maximum length of the merged sequence

may be specified with the \-\-fastq_minmergelen and

\-\-fastq_maxmergelen options, respectively. Other relevant options

are: \-\-fastq_ascii, \-\-fastq_maxee, \-\-fastq_nostagger,

\-\-fastq_qmax, \-\-fastq_qmaxout, \-\-fastq_qmin, \-\-fastq_qminout,

.RE

.PP

.\" ----------------------------------------------------------------------------

Taxonomic classification options:

.RS

The vsearch command \-\-sintax will classify the input sequences

according to the Sintax algorithm as described by Robert Edgar (2016)

in SINTAX: a simple non-Bayesian taxonomy classifier for 16S and ITS

sequences, BioRxiv, 074161. Preprint. doi: https://doi.org/10.1101/074161.

The name of the fasta file containing the input sequences to be

classified is given as an argument to the \-\-sintax command. The reference

sequence database is specified with the \-\-db option. The results are

written in a tab delimited text file whose name is specified with the

\-\-tabbedout option. The \-\-sintax_cutoff option may be used to set a

minimum level of bootstrap support for the taxonomic ranks to be reported.

Multithreading is supported. Databases in UDB files are supported.

The strand option may be specified.

The reference database must contain taxonomic information in the

header of each sequence in the form of a string starting with ";tax="

and followed by a comma-separated list of up to eight taxonomic

identifiers. Each taxonomic identifier must start with an indication

of the rank by one of the letters d (for domain) k (kingdom), p

(phylum), c (class), o (order), f (family), g (genus), or s

(species). The letter is followed by a colon (:) and the name of that

rank. Commas and semicolons are not allowed in the name of the rank.

Example: ">X80725_S000004313;tax=d:Bacteria,p:Proteobacteria,c:Gammaproteobacteria,o:Enterobacteriales,f:Enterobacteriaceae,g:Escherichia/Shigella,s:Escherichia_coli".

.PP

.TP 9

.BI \-\-db \0filename

Read the reference sequences from \fIfilename\fR, in FASTA, FASTQ or UDB format. These sequences needs to be annotated with taxonomy.

.TP

.BI \-\-sintax_cutoff\~ "real"

Specify a minimum level of bootstrap support for the taxonomic ranks that will be included in column 4 of the output file. For instance 0.9, corresponding to 90%.

.TP

.BI \-\-sintax \0filename

Read the input sequences from \fIfilename\fR, in FASTA or FASTQ format.

.TP

.BI \-\-tabbedout \0filename

Write the results to \fIfilename\fR, in a tab-separated text

format. Column 1 contains the query label. Column 2 contains the

predicted taxonomy in the same format as for the reference data, with

bootstrap support indicated in parentheses after each rank. Column 3

contains the strand. If the \-\-sintax_cutoff option is used, the

predicted taxonomy will be repeated in column 4 while omitting the

bootstrap values and including only the ranks with support at or above

the threshold.

.RE

.PP

.\" ----------------------------------------------------------------------------

UDB options:

.RS

Databases to be used with the \-\-usearch_global command may be

.PP

.\" ============================================================================

.SH COPYRIGHT

Copyright (C) 2014-2017, Torbjørn Rognes, Frédéric Mahé and Tomás

Copyright (C) 2014-2018, Torbjørn Rognes, Frédéric Mahé and Tomás

Flouri

.PP

All rights reserved.

Fix several bugs on Windows related to large files, use of "-" as a

file name to mean stdin or stdout, alignment errors, missed kmers and

corrupted UDB files. Added documentation of UDB-related commands.

.TP

.BR v2.7.2\~ "released April 20th, 2018"

Added the sintax command for taxonomic classification. Fixed a bug with

incorrect FASTA headers of consensus sequences after clustering.

.TP

.BR v2.8.0\~ "released April 24th, 2018"

Added the fastq_maxdiffpct option to the fastq_mergepairs command.

.RE

.LP

.\" ============================================================================

showalign.h \

sha1.h \

shuffle.h \

sintax.h \

sortbylength.h \

sortbysize.h \

subsample.h \

sha1.c \

showalign.cc \

shuffle.cc \

sintax.cc \

sortbylength.cc \

sortbysize.cc \

subsample.cc \