DESCRIPTION

NAME mapsembler, version 2.0.5.deb - 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

-n node_len: limit max of nodes length. Default: 1000000

-l 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 LARGEUR or PROFONDEUR. Default: LARGEUR

-m file_name: write in file "file_name" the reads mapped on starters

-h prints this message and exit