Scroll to navigation

MAPSEMBLER_EXTEND(1) User Commands MAPSEMBLER_EXTEND(1)

NAME

mapsembler_extend - extends a DNA sequence of interest given a set of reads, by computing a targeted micro assembly

SYNOPSIS

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]

DESCRIPTION

Mapsembler 2 extends a DNA sequence of interest given a set of reads, by computing a targeted micro assembly.

OPTIONS

-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

-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

-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

-x node_len: limit max of nodes length. Default: 40

-y graph_max_depth: limit max of graph depth.Default: 10000

-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"

-p search_mod: kind of prosses Breadth or Depth. Default: Breadth

-h prints this message and exit

AUTHOR

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.

October 2018 mapsembler_extend 2.2.4