Mapsembler 2 is a software that extends a DNA sequence of interest given a set of reads.
First, Mapsembler 2 determines if each starter is read-coherent, e.g. whether reads confirm the presence of each starter in the original sequence. Then, Mapsembler2 uses Minia to extend each read-coherent starter. Mapsembler2 outputs its sequence neighborhood as a linear sequence or as a graph, depending on the user choice.
After reads are mapping on Mapsembler2 output graph and add an average coverage on each edges and each nodes. The graph elements with average coverage lower than the minimum coverage define by the user) has been removed.
Finally,the output graph of Mapsembler 2 and Phaser can be visualized with Graph Sequence Viewer (GSV).
Mapsembler2 may be used for (not limited to):
- Validate an assembled sequence (input as starter), e.g. from a de Bruijn graph assembly where read-coherence was not enforced.
- Checks if a gene (input as starter) has an homolog in a set of reads
- Checks if a known enzyme is present in a metagenomic NGS read set.
- Enrich unmappable reads by extending them, possibly making them mappable
- Checks what happens at the extremities of a contig
- Remove contaminants or symbiont reads from a read set
More details here
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-- Mapsembler 2 authors
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