GenSeed is a tool that allows for targeted assembly of specific sequences in the genome using reads relevant to the targets. This Perl program implements a recursive algorithm to find sequence similarity, select reads, and assembly. The program should be useful for assembling particular nuclear genes, transcripts and extrachromosomal genomes.
Sobreira TJ, Gruber A "Sequence-specific reconstruction from fragmentary databases using seed sequences: implementation and validation on SAGE, proteome and generic sequencing data." Bioinformatics. 2008 Aug 1;24(15):1676-80. Epub 2008 Jun 9. https://doi.org/10.1093/bioinformatics/btn283
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