Mapsembler
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Application data |
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| Created by | Peterlongo P, Chikhi R |
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| Biological application domain(s) | Metagenomics, Transcriptomics, Sequencing, RNA-Seq quantification, Exome capture |
| Principal bioinformatics method(s) | Sequence assembly, Sequence assembly, Read mapping |
| Technology | Illumina, 454 |
| Created at | IRISA-Symbiose, INRIA Rennes - Bretagne Atlantique Symbiose team |
| Maintained? | Yes |
| Input format(s) | FASTA |
| Output format(s) | FASTA, XGMML (Cytoscape), graphml (Gephi) |
| Software features | De novo assembly, Identify Novel Exons, Remove contaminants, Detect enzymes in metagenomics NGS reads |
| Programming language(s) | C |
| Licence | CeCILL |
| Operating system(s) | Linux |
Summary: 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.
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Description
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
Links
References
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