.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.45.1.
.TH MAPSEMBLER "1" "June 2014" "mapsembler 2.1.6+dfsg" "User Commands"
.SH NAME
mapsembler \- manual page for mapsembler 2.1.6+dfsg
.SH DESCRIPTION
NAME
mapsembler, version 2.0.5.deb \- Copyright INRIA \- CeCILL License
.PP
SYNOPSIS
\&./maps/mapsembler <starters.fasta> <readsC1.fasta> [<readsC2.fasta> [<readsC3.fasta] ...] [\-E] [\-t extension_type] [\-q value] [\-k value] [\-c value] [\-d authorized_distance] [\-e error_threshold] [\-g value] [\-i index_name] [\-o name] [\-m name] [\-h]
.PP
DESCRIPTION
.IP
Mapsembler2 is a targeted assembly software. It takes as input a set of NGS raw reads (fasta or fastq, gzipped or not) and a set of input sequences (starters). It first determines if each starter is read\-coherent, e.g. whether reads confirm the presence of each starter in the original sequence. Then for each read\-coherent starter, Mapsembler2 outputs its sequence neighborhood as a linear sequence or as a graph, depending on the user choice.
.PP
OPTIONS
.HP
\fB\-E\fR Extend only: avoid the mapping+substarter generation phase
.HP
\fB\-t\fR extension_type. Default: 1
.IP
1: a strict sequence: any branching stops the extension
2: a consensus sequence: contiging approach
3: a strict graph: any branching is conserved in the graph
4: a consensus graph: "small" polymorphism is merged, but "large" structures are represented
.HP
\fB\-q\fR size_seed: will use seeds of length size_seed during the mapping process. Default: 25, value should be in [5\-31]
.HP
\fB\-k\fR size_kmers: Size of the k\-mers used duriung the extension phase Default: 31. Accepted range, depends on the compilation (make k=42 for instance)
.HP
\fB\-c\fR min_coverage: a sequence is covered by at least min_coverage coherent reads. Default: 2
.HP
\fB\-d\fR authorized_distance: a substarter is distant by at most authorized_distance substitutions. Default: 2
.HP
\fB\-e\fR error_threshold: a nucleotide is corrected if occurs less than error_threshold times. Default: 2
.HP
\fB\-g\fR estimated_genome_size: estimation of the size of the genome whose reads come from.
.IP
It is in bp, does not need to be accurate, only controls memory usage. Default: 3 billion
.HP
\fB\-n\fR node_len: limit max of nodes length. Default: 1000000
.HP
\fB\-l\fR graph_max_depth: limit max of graph depth.Default: 10000
.HP
\fB\-i\fR index_name: stores the index files in files starting with this prefix name. Can be re\-used latter. Default: "index"
.IP
IF THE FILE "index_name.bloom" EXISTS: the index is not re\-created
.HP
\fB\-o\fR file_name_prefix: where to write outputs. Default: "res_mapsembler"
.HP
\fB\-p\fR search_mod: kind of prosses LARGEUR or PROFONDEUR. Default: LARGEUR
.HP
\fB\-m\fR file_name: write in file "file_name" the reads mapped on starters
.HP
\fB\-h\fR prints this message and exit
.SH "SEE ALSO"
The full documentation for
.B mapsembler
is maintained as a Texinfo manual.  If the
.B info
and
.B mapsembler
programs are properly installed at your site, the command
.IP
.B info mapsembler
.PP
should give you access to the complete manual.