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ALLPATHS is a tool for genome assembly that is applicable to all types of sequences and not limited to just short reads. It performs paired-read assembly in 2 stages: (i) finding all paths across a read pair, which involves filling the gap between each paired end read with other paired end reads, (ii) grouping together paired ends from the previous step and assemble each of these groups separately before assembling all of them to form the final assembly.


Sequence assembly



Butler J, MacCallum I, Kleber M, Shlyakhter IA, Belmonte MK, Lander ES, Nusbaum C, Jaffe DB "ALLPATHS: de novo assembly of whole-genome shotgun microreads." Genome Res. 2008 May;18(5):810-20.
PMID: 18340039
PMCID: PMC2336810

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