.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.7.
.TH MAPSEMBLER_EXTEND "1" "October 2018" "mapsembler_extend 2.2.4" "User Commands"
.SH NAME
mapsembler_extend \- extends a DNA sequence of interest given a set of reads, by computing a targeted micro assembly
.SH SYNOPSIS
.B mapsembler_extend
<extrem_kmers.fasta> <readsC1.fasta> [<readsC2.fasta> [<readsC3.fasta] ...] [\-t extension_type] [\-k value] [\-c value] [\-g value] [\-i index_name] [\-o name] [\-h]
.SH DESCRIPTION
Mapsembler 2 extends a DNA sequence of interest given a set of reads, by computing a targeted micro assembly.
.SH OPTIONS
.HP
\fB\-t\fR extension_type. Default: 1
.IP
1: a strict sequence: any branching stops the extension
.IP
2: a consensus sequence: contiging approach
.IP
3: a strict graph: any branching is conserved in the graph
.IP
4: a consensus graph: "small" polymorphism is merged, but "large" structures are represented
.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\-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\-x\fR node_len: limit max of nodes length. Default: 40
.HP
\fB\-y\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 Breadth or Depth. Default: Breadth
.HP
\fB\-h\fR prints this message and exit
.SH AUTHOR
This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.