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Short description:
Please summarise the application in a few sentences. Avoid links here. Mapsembler is a targeted assembly software. It takes as input a set of NGS raw reads 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, Mapsembler outputs its sequence neighborhood as a linear sequence or as a graph, depending on the user choice.
Software version:
Biological application domain(s) (Phylogenetics, Genomics, ...):
Metagenomics, Transcriptomics, Sequencing, RNA-Seq quantification, Exome capture,
Principal bioinformatics method(s) (Assembly, Mapping, ...):
Sequence assembly, Sequence assembly, Read mapping,
Technology (Sanger, Illumina, 454, SOLiD, Ion Torrent, ...):
Illumina, 454,
Interface (Command line, Web UI, Desktop GUI, SOAP WS, HTTP WS, API, QL):
Resource type (Command-line tool, Web application, Desktop application, Script, Suite, Workbench, Database portal, Workflow, Plug-in, Library, Web API, Web service, SPARQL endpoint):
IRISA-Symbiose, INRIA Rennes - Bretagne Atlantique Symbiose team
== Description == <!-- Describe the application in the space below --> Mapsembler page Description and possible usages: Mapsembler is a targeted micro-assembly software. It takes as input a set of NGS raw reads 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, Mapsembler outputs its sequence neighborhood as a linear sequence or as a graph, depending on the user choice. Mapsembler may be used for (not limited to): · Validate an assembly (the starter) based on de-Bruijn graph where read-coherence was not enforced. · Checks if a gene (the starter) as an homolog in a set of reads · Checks if a known enzyme is present in a metagenomic NGS read set. · Enrich unmappable reads before to try to map them with their neighbors · Checks what appends at the extremities of a contig · Remove contaminants or symbiont reads from a read set <!-- -->
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