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docs/README.rst

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+AdapterRemoval v2
+=================
+
+.. image:: https://img.shields.io/travis/MikkelSchubert/adapterremoval/master.svg
+    :target: https://travis-ci.org/MikkelSchubert/adapterremoval
+    :alt: Travis-CI
+
+.. image:: https://img.shields.io/coveralls/MikkelSchubert/adapterremoval.svg
+    :target: https://coveralls.io/github/MikkelSchubert/adapterremoval
+    :alt: Coveralls
+
+AdapterRemoval searches for and removes adapter sequences from High-Throughput
+Sequencing (HTS) data and (optionally) trims low quality bases from the 3' end
+of reads following adapter removal. AdapterRemoval can analyze both single end
+and paired end data, and can be used to merge overlapping paired-ended reads
+into (longer) consensus sequences. Additionally, AdapterRemoval can construct a
+consensus adapter sequence for paired-ended reads, if which this information is
+not available.
+
+If you use AdapterRemoval v2, then please cite the paper
+
+    Schubert, Lindgreen, and Orlando (2016). AdapterRemoval v2: rapid adapter
+    trimming, identification, and read merging. BMC Research Notes, 12;9(1):88
+    http://bmcresnotes.biomedcentral.com/articles/10.1186/s13104-016-1900-2
+
+AdapterRemoval was originally published in Lindgreen 2012:
+
+    Lindgreen (2012): AdapterRemoval: Easy Cleaning of Next Generation
+    Sequencing Reads, BMC Research Notes, 5:337
+    http://www.biomedcentral.com/1756-0500/5/337/
+
+
+Overview of major features
+==========================
+
+ - Trimming of adapters sequences from single-end and paired-end FASTQ reads.
+ - Trimming of multiple, different adapters or adapter pairs.
+ - Demultiplexing of single or double indexed reads, with or without trimming
+   of adapter sequences.
+ - Reconstruction of adapter sequences from paired-end reads, by the pairwise
+   alignment of reads in the absence of a known adapter sequence.
+ - Merging of overlapping read-pairs into higher-quality consensus sequences.
+ - Multi-threading of all operations for increased throughput.
+ - Reading and writing of gzip and bzip2 compressed files.
+ - Reading and writing of interleaved FASTQ files.
+
+
+Installation
+============
+
+For detailed installation instructions, please see the
+`Installation <https://adapterremoval.readthedocs.io/en/latest/installation.html>`_
+section of the online documentation.
+
+Installing AdapterRemoval using `Conda <https://conda.io/docs/>`_
+-----------------------------------------------------------------
+
+If you have Conda `installed on your system <https://conda.io/miniconda.html>`_,
+you may install AdapterRemoval using one of serveral unoffical recipies::
+
+    conda install -c bioconda adapterremoval
+    conda install -c maxibor adapterremoval2
+
+
+Installing AdapterRemoval on Debian based systems
+-------------------------------------------------
+
+Users of Debian Stretch or Ubuntu Artful Aardvark may install AdapterRemoval
+using Apt::
+
+    sudo apt-get install adapterremoval adapterremoval-examples
+
+
+Building AdapterRemoval from scratch
+------------------------------------
+
+Compiling AdapterRemoval from scratch requires a C++11 compliant compiler, and
+that the zlib and bz2lib headers are installed::
+
+    make
+    sudo make install
+
+
+Getting started
+===============
+
+To run AdapterRemoval, specify the location of pair 1 and (optionally) pair 2
+FASTQ using the --file1 and --file2 command-line options::
+
+    AdapterRemoval --file1 myreads_1.fastq.gz --file2 myreads_2.fastq.gz
+
+By default, AdapterRemoval will save the trimmed reads in the current working
+directly, using filenames starting with 'your_output'. See the
+`Input and Output
+<https://adapterremoval.readthedocs.io/en/latest/input_and_output.html>`_
+files section for more information about files generated by AdapterRemoval.
+
+More examples of common usage may be found in the
+`Examples <https://adapterremoval.readthedocs.io/en/latest/examples.html>`_
+section of the online documentation.
+
+
+Documentation
+-------------
+
+For a detailed description of program usage, please refer to the online
+`online documentation <https://adapterremoval.readthedocs.io/>`_.

docs/input_and_output.rst

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+Input and output files
+======================
+
+
+Output files
+------------