Commit 65c61e44 authored by Andreas Tille's avatar Andreas Tille
Browse files

New upstream version 3.1.0

parent b166ffcb

CMakeLists.txt

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@@ -2,7 +2,7 @@ cmake_minimum_required( VERSION 2.8.2 ) 


project( FLEXBAR )



set( SEQAN_APP_VERSION "3.0.3" )

set( SEQAN_APP_VERSION "3.1.0" )



include_directories( ${FLEXBAR_SOURCE_DIR}/include )

# link_directories( ${FLEXBAR_SOURCE_DIR}/lib )

LICENSE.md

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BSD 3-Clause License



Copyright (c) 2017, SeqAn

Copyright (c) 2018, SeqAn

All rights reserved.



Redistribution and use in source and binary forms, with or without

README.md

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## Flexbar — flexible barcode and adapter removal

## Flexbar – flexible barcode and adapter removal



The program Flexbar preprocesses high-throughput sequencing data efficiently. It demultiplexes barcoded runs and removes adapter sequences. Moreover, trimming and filtering features are provided. Flexbar increases read mapping rates and improves genome as well as transcriptome assemblies. It supports next-generation sequencing data in fasta and fastq format, e.g. from Roche 454 and the Illumina platform.

The program Flexbar preprocesses high-throughput sequencing data efficiently. It demultiplexes barcoded runs and removes adapter sequences. Moreover, trimming and filtering features are provided. Flexbar increases read mapping rates and improves genome as well as transcriptome assemblies. Unique molecular identifiers can be extracted in a flexible way. The program supports sequencing data in fasta and fastq format, e.g. from the Illumina platform.



Refer to the [manual](https://github.com/seqan/flexbar/wiki) or contact [jtroehr](https://github.com/jtroehr) for support with this application.

Refer to the [manual](https://github.com/seqan/flexbar/wiki) or contact [Johannes Roehr](https://github.com/jtroehr) for support with this application.



![Flexbar logo](https://github.com/seqan/flexbar/wiki/images/flexbar-logo.png)





### Reference

### References



Matthias Dodt, Johannes T. Roehr, Rina Ahmed, Christoph Dieterich: Flexbar — flexible barcode and adapter processing for next-generation sequencing platforms. Biology 2012, 1(3):895-905.

Johannes T. Roehr, Christoph Dieterich, Knut Reinert: Flexbar 3.0 – SIMD and multicore parallelization. Bioinformatics 2017.



See article on [PubMed](http://www.ncbi.nlm.nih.gov/pubmed/24832523).

See article on [PubMed](https://www.ncbi.nlm.nih.gov/pubmed/28541403)



Matthias Dodt, Johannes T. Roehr, Rina Ahmed, Christoph Dieterich: Flexbar – flexible barcode and adapter processing for next-generation sequencing platforms. Biology 2012.



See article on [PubMed](https://www.ncbi.nlm.nih.gov/pubmed/24832523)





### Download
@@ -21,23 +25,23 @@ Flexbar source code as well as binaries for Linux and Mac OS can be downloaded o 


### Building from source



Make sure that `cmake` is available, as well as development and runtime files of the TBB library 4.0 or later (Intel Threading Building Blocks). Using a package manager is a simple way to install them. Furthermore, the SeqAn library and a compiler that supports C++14 is required:

Make sure that `cmake` is available, as well as development and runtime files of the TBB library 4.0 or later (Intel Threading Building Blocks). For example on Debian systems, install the packages `libtbb-dev` and `libtbb2`. Furthermore, the SeqAn library and a compiler that supports C++14 is required:



* Get SeqAn library version 2.2.0 [here](https://github.com/seqan/seqan/releases/download/seqan-v2.2.0/seqan-library-2.2.0.tar.xz)

* Download Flexbar 3.0.3 source code [release](https://github.com/seqan/flexbar/releases)

* Download Flexbar 3.1 source code [release](https://github.com/seqan/flexbar/releases)



Decompress both files:



		tar xzf flexbar-3.0.3.tar.gz

	tar xzf flexbar-3.1.0.tar.gz

	tar xJf seqan-library-2.2.0.tar.xz



Move SeqAn include folder to Flexbar:



        mv seqan-library-2.2.0/include flexbar-3.0.3

	mv seqan-library-2.2.0/include flexbar-3.1.0



Use these commands for building:



        cd flexbar-3.0.3

	cd flexbar-3.1.0

	cmake .

	make

src/CMakeLists.txt

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@@ -59,12 +59,3 @@ endif() 
# endif()



set( SEQAN_CTD_EXECUTABLES ${SEQAN_CTD_EXECUTABLES} flexbar CACHE INTERNAL "" )
 


# set( CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} "/Users/jtr/Downloads/seqan-trunk/util/cmake" )

# set( SEQAN_FIND_DEPENDENCIES ZLIB BZip2 )

# find_package( SeqAn REQUIRED )



# add_definitions( ${SEQAN_DEFINITIONS} )

# include_directories( ${SEQAN_INCLUDE_DIRS} )

# target_link_libraries( flexbar ${SEQAN_LIBRARIES} )

# set( SEQAN_HAS_ZLIB FALSE )

src/Flexbar.cpp

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   Flexbar - flexible barcode and adapter removal

   

   Version 3.0.3

   Version 3.1.0

   

   uses SeqAn library release 2.2.0

   and TBB library 4.0 or later
@@ -27,8 +27,8 @@ int main(int argc, const char* argv[]){ 
	using namespace std;

	using namespace seqan;

	

	const string version = "3.0.3";

	const string date    = "May 2017";

	const string version = "3.1";

	const string date    = "April 2018";

	

	ArgumentParser parser("flexbar");