New upstream version 3.2.1

    ARGS "rev-parse --short HEAD"

    OUTPUT_VARIABLE VERSION_SHA1 )

if ( VERSION_SHA1 MATCHES "^[0-9a-f]+$") # might return "git commit fatal: not a git repository"

    message("Git version: ${VERSION_SHA1}")

    add_definitions( -DGIT_SHA1="${VERSION_SHA1}" )

endif()

################################################################################

# Define cmake modules directory

target_link_libraries("merci" ${gatb-core-libraries})

# that file will hold the version information as a #define

configure_file (

${PROJECT_SOURCE_DIR}/src/build_info.hpp.in

${PROJECT_SOURCE_DIR}/src/build_info.hpp

)

################################################################################

#  DOC

################################################################################

# run tests

echo "Running simple test..."

cd test

. ./simple_test.sh

./simple_test.sh

cd ..

Type `minia` without any arguments for usage instructions.

A more complete manual:

    cd doc 

    pdflatex manual.tex

If you cannot compile it: http://minia.genouest.org/files/minia.pdf

A more complete manual is here: https://github.com/GATB/minia/raw/master/doc/manual.pdf

# What is new ? (2018)

\documentclass[a4paper]{article}

\usepackage{fancyvrb}

\usepackage{pdfpages}

\usepackage{hyperref}

\usepackage{url}

\begin{document}

\begin{description}

\vitem+kmer-size+

The $k$-mer length is the length of the nodes in the de Bruijn graph. It strongly depends on the input dataset. For proper assembly, we recommend that you use the Minia-pipeline that runs Minia multiple times, with an iterative multi-k algorithm. That way, you won't need to choose k. If you insist on running with a single k value, the KmerGenie software can automatically find the best $k$ for your dataset.

        The $k$-mer length is the length of the nodes in the de Bruijn graph. It strongly depends on the input dataset. For proper assembly, we recommend that you use the Minia-pipeline (\url{https://github.com/GATB/gatb-minia-pipeline}) that runs Minia multiple times, using an iterative multi-k algorithm (similar to IDBA, Megahit). That way, you won't need to choose k. If you insist on running with a single k value, the KmerGenie software can automatically find the best $k$ for your dataset.

\vitem+abundance-min+

The \verb+abundance-min+ is a hard cut-off to remove likely erroneous, low-abundance $k$-mers. In Minia 3, it is recommended to set it to 2 unless you have a good reason not to. Minia 3 also implements other ways to remove erroneous k-mers, using a more adequate relative cut-off, in the graph simplifications step.

\section{Output}

The output of Minia is a set of contigs in the FASTA format, in the file \verb+[prefix].contigs.fa+. 

\subsection{Fasta}

\subsection*{Creating unitigs}

The main output of Minia is a set of contigs in the FASTA format, in the file \verb+[prefix].contigs.fa+. 

Minia will also output unitigs in the FASTA format. Those are non-branching paths in the de Bruijn graph prior to any graph simplification. File: \verb+[prefix].unitigs.fa+. 

\subsection{Assembly graph}

The contigs FASTA file can be converted to GFA using \href{https://github.com/GATB/bcalm/blob/master/scripts/convertToGFA.py}{BCALM's convertToGFA.py script}.

\subsection*{Unitigs}

Minia will also output unitigs, in the FASTA format. They correspond to non-branching paths in the de Bruijn graph prior to any graph simplification. File: \verb+[prefix].unitigs.fa+. 

\section{Selection of graph simplification steps}