Mapsembler is a tool for targeted assembly of particular genomic locus using short reads. It implements an algorithm to estimate occurrences of a sequence of interest among reads and build an extension graph from matching reads. This tool can be used to target repeats, SNPs, exon skipping, gene fusion and other structural variants without the need to assemble the entire genome.
Sequence assembly
Peterlongo P, Chikhi R "Mapsembler, targeted and micro assembly of large NGS datasets on a desktop computer." BMC Bioinformatics. 2012 Mar 23;13:48. https://doi.org/10.1186/1471-2105-13-48
PMID: 22443449
PMCID: PMC3514201
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