Provided by: mapsembler2_2.0.5+dfsg-2_amd64 
NAME
mapsembler - manual page for mapsembler 2.0.5+dfsg
DESCRIPTION
NAME mapsembler, version 2.0.4 - Copyright INRIA - CeCILL License
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]
DESCRIPTION
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.
OPTIONS
-E Extend only: avoid the mapping+substarter generation phase
-t extension_type. Default: 1
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
-q size_seed: will use seeds of length size_seed during the mapping process. Default: 25, value should be
in [5-31]
-k 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)
-c min_coverage: a sequence is covered by at least min_coverage coherent reads. Default: 2
-d authorized_distance: a substarter is distant by at most authorized_distance substitutions. Default: 2
-e error_threshold: a nucleotide is corrected if occurs less than error_threshold times. Default: 2
-g estimated_genome_size: estimation of the size of the genome whose reads come from.
It is in bp, does not need to be accurate, only controls memory usage. Default: 3 billion
-i index_name: stores the index files in files starting with this prefix name. Can be re-used latter.
Default: "index"
IF THE FILE "index_name.bloom" EXISTS: the index is not re-created
-o file_name_prefix: where to write outputs. Default: "res_mapsembler"
-m file_name: write in file "file_name" the reads mapped on starters
-h prints this message and exit
SEE ALSO
The full documentation for mapsembler is maintained as a Texinfo manual. If the info and mapsembler
programs are properly installed at your site, the command
info mapsembler
should give you access to the complete manual.