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, DNA-Seq, RNA-Seq Quantitation, Targeted assembly |
| Principal bioinformatics method(s) | Assembly, micro assembly, Mapping |
| Technology | Solexa, 454 |
| Created at | IRISA-Symbiose, INRIA Rennes - Bretagne Atlantique Symbiose team |
| Maintained? | Yes |
| Input format(s) | FASTA |
| 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 explores a set of NGS raw reads, trying to reconstruct an input sequence fragment (the starter). In case of success, we say that the starter is “read coherent”. In this case, Mapsembler outputs flanking neighbors as a linear sequence or as a graph, depending on the user’s choices.
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Description
Mapsembler page Description and possible usages:
Mapsembler explores a set of NGS raw reads, trying to reconstruct an input sequence fragment (the starter). In case of success, we say that the starter is “read coherent”. In this case, Mapsembler outputs flanking neighbors as a linear sequence or as a graph, depending on the user’s choices. 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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