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By Jackman S., Birol I., Last update 1494698999
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AdjList description

AdjList finds overlaps of [m,k) bases. Contigs are read from files. Overlaps of exactly k-1 bases are found using a hash table. Overlaps of fewer than k-1 bases are found using a suffix array.

Parent program: abyss

ABySS is a de novo sequencing assembler developed for short reads of large genomes. It has novel scaffolding algorithm capable of assembling very large genomes including human genomes (>3.5 billion paired-end reads). ABySS algorithm eliminates ambiguities in the scaffold graph and identifies contigs that are assembled into scaffolds.The assembly runs in three stages: assemble contigs without paired-end information, align the paired-end reads to the initial assembly, and merge contigs joined by paired-end information.