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A

assemble() - Method in class Assembler

Assembles a genome sequence based on a dictionary of k-mers.

Assembler - Class in <Unnamed>

The Assembler application assembles a genome from a set of short sequencing reads.

Assembler(String) - Constructor for class Assembler

Creates an Assembler that builds a genome assembly from a file of sequencing reads.

E

extendGenomeSequenceBackward() - Method in class Assembler

Attempts to extend the genome sequence backward (to the left) repeatedly, one character at a time.

extendGenomeSequenceForward() - Method in class Assembler

Attempts to extend the genome sequence forward (to the right) repeatedly, one character at a time.

M

main(String[]) - Static method in class Assembler

The main method executes the Assembler on a file of sequencing reads.

P

populate_kmer_dictionary(String) - Method in class Assembler

Reads in a file of sequencing reads.

T

toString() - Method in class Assembler

Returns a String representation of the assembly, i.e., returns the assembled genome sequence.

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