mapsembler2_extend1
Extends a dna sequence of interest given a set of reads, by computing a targeted micro assembly
Part of mapsembler_extend(1).
Usage
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]
Overview
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
Releases
Unchanged in 4 releases since Debian 10 (Buster).