Difference between revisions of "Mapsembler"
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{{Bioinformatics application | {{Bioinformatics application | ||
− | |sw summary=Mapsembler | + | |sw 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. |
− | |bio domain=Metagenomics, Transcriptomics, | + | |bio domain=Metagenomics, Transcriptomics, Sequencing, RNA-Seq quantification, Exome capture, |
− | |bio method= | + | |bio method=Sequence assembly, Sequence assembly, Read mapping, |
− | |bio tech= | + | |bio tech=Illumina, 454, |
|created by=Peterlongo P, Chikhi R | |created by=Peterlongo P, Chikhi R | ||
|created at=IRISA-Symbiose, INRIA Rennes - Bretagne Atlantique Symbiose team | |created at=IRISA-Symbiose, INRIA Rennes - Bretagne Atlantique Symbiose team | ||
|maintained=Yes | |maintained=Yes | ||
|input format=FASTA, | |input format=FASTA, | ||
− | |output format=FASTA, XGMML (Cytoscape) | + | |output format=FASTA, XGMML (Cytoscape), graphml (Gephi) |
|sw feature=De novo assembly, Identify Novel Exons, Remove contaminants, Detect enzymes in metagenomics NGS reads | |sw feature=De novo assembly, Identify Novel Exons, Remove contaminants, Detect enzymes in metagenomics NGS reads | ||
|language=C, | |language=C, | ||
Line 21: | Line 21: | ||
Description and possible usages: | Description and possible usages: | ||
− | Mapsembler | + | 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. | · Validate an assembly (the starter) based on de-Bruijn graph where read-coherence was not enforced. |
Latest revision as of 20:43, 19 December 2015
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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