MAPseq v1.0 (14 October 2016)
by Joao F. Matias Rodrigues, Thomas S.B. Schmidt, Janko Tackmann, and Christian von Mering
Institute of Molecular Life Sciences, University of Zurich, Switzerland
Matias Rodrigues JF, Schmidt TSB, Tackmann J, Mering C von. MAPseq: bringing speed, accuracy and consistency to metagenomic ribosomal RNA analysis. submitted.
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Table of contents

1. Installation
2. MAPseq usage instructions
3. File output
 a) The results file
 b) Obtaining taxonomies from the results
 c) Obtaining OTU classification from the results
4. FAQ
6. History

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MAPseq is a set of very fast and accurate tools designed to classify raw sequence reads of ribosomal
RNA sequences in terms of their taxonomy and OTU classification. This is done by using a
reference set of full-length ribosomal RNA sequences for which known taxonomies are known,
and for which a set of high quality OTU clusters has been previously generated.
For each read, the best guess and correspoding confidence in the assignment is shown at
each taxonomic and OTU level.

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For bugs and more information contact: Joao F. Matias Rodrigues <jfmrod@gmail.com>


1. INSTALLATION
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You can get the source code or binary packages at:

http://meringlab.org/software/mapseq/

or clone it using git using the command:

git clone https://github.com/jfmrod/mapseq.git


i) To compile on Linux/Unix/MacOSX type the following in the source directory

./bootstrap     # this step is only needed if you cloned the repository, you will also need to install autotools/autoconf packages
./configure
make
make install

In the directory where you unpacked the package contents.
Alternatively, if you want the program to be installed to another
location instead of the default system wide /usr/local/ directory,
you can change the ./configure command to:

./configure --prefix=$HOME/usr

This would install the program binaries to a directory usr/bin inside
your home directory (i.e.: $HOME/usr/bin/mapseq), after you type
the command "make install".


2. MAPseq usage instructions
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a) USING MAPseq
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MAPseq takes as input a fasta file with raw sequence data which should have been previously
demultiplexed and quality filtered usually from a fastq file produced by the sequencing machine.

If the input sequences can be found in the file "rawseqs.fa". Then to classify the reads
one simply has to run the following command:

mapseq rawseqs.fa > rawseqs.fa.mseq

This will classify all the sequences found in rawseqs against the standard reference dataset
provided with MAPseq.

You can change the number of threads that MAPseq uses with the -nthreads <no_threads> argument.


3. FILE OUTPUT
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a) THE RESULTS FILE
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In the results output, each line indicates a classification of the read. 

TODO


b) OBTAINING A CONFIDENT TAXONOMY FROM THE RESULTS FILE
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Once result file has been computed, you can produce a confident taxonomic assignment by ...

TODO


c) OBTAINING A CONFIDENT OTU ASSIGNMENT
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TODO

4. FAQ
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Frequently asked questions and other documentation can be found at
http://meringlab.org/software/mapseq/faq.html


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6. HISTORY

1.0.0 (14 October 2016)
- First release of MAPseq