Class Assembler

java.lang.Object

Assembler

public class Assembler
extends java.lang.Object

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

Constructor Summary

Constructors

Constructor and Description
Assembler(java.lang.String filename) Creates an Assembler that builds a genome assembly from a file of sequencing reads.

Method Summary

Methods

Modifier and Type	Method and Description
void	assemble() Assembles a genome sequence based on a dictionary of k-mers.
void	extendGenomeSequenceBackward() Attempts to extend the genome sequence backward (to the left) repeatedly, one character at a time.
void	extendGenomeSequenceForward() Attempts to extend the genome sequence forward (to the right) repeatedly, one character at a time.
static void	main(java.lang.String[] args) The main method executes the Assembler on a file of sequencing reads.
void	populate_kmer_dictionary(java.lang.String filename) Reads in a file of sequencing reads.
java.lang.String	toString() Returns a String representation of the assembly, i.e., returns the assembled genome sequence.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

Assembler

public Assembler(java.lang.String filename)

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

Parameters:

filename - the name of the file containing sequencing reads

Method Detail

toString

public java.lang.String toString()

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

Overrides:

toString in class java.lang.Object

Returns:

a String representation of the genome assembly

populate_kmer_dictionary

public void populate_kmer_dictionary(java.lang.String filename)

Reads in a file of sequencing reads. For each k-mer in a sequencing read, the k-mer is added to the dictionary and the number of occurrences of the k-mer is updated appropriately.

Parameters:

filename - the name of the file containing sequencing reads

assemble

public void assemble()

Assembles a genome sequence based on a dictionary of k-mers. As a starting point, one k-mer from the dictionary is chosen. This k-mer is extended forward as long as possible, one character at a time, into a growing genome sequence. When the genome sequence cannot be extended further forward, then the genome sequence is extended backward as long as possible, one character at a time.

extendGenomeSequenceForward

public void extendGenomeSequenceForward()

Attempts to extend the genome sequence forward (to the right) repeatedly, one character at a time. The genome sequence is extended and a character added to its end if there exists a nucleotide character that can be added to the end of the k-1 final characters of the genome sequence to form a k-mer that occurs in the k-mer dictionary. If there are multiple individual nucleotide characters that can be added to the final k-1 characters in the genome sequence to form k-mers in the dictionary, then the character resulting in the k-mer with the largest number of occurrences in the dictionary is chosen. Each time the genome sequence is extended by a character, the corresponding k-mer is removed from the dictionary so that it will not be used in future extensions.

extendGenomeSequenceBackward

public void extendGenomeSequenceBackward()

Attempts to extend the genome sequence backward (to the left) repeatedly, one character at a time. The genome sequence is extended and a character added to its front if there exists a nucleotide character that can be added to the front of the k-1 first characters of the genome sequence to form a k-mer that occurs in the k-mer dictionary. If there are multiple individual nucleotide characters that can be prepended to the first k-1 characters in the genome sequence to form k-mers in the dictionary, then the character resulting in the k-mer with the largest number of occurrences in the dictionary is chosen. Each time the genome sequence is extended by a character, the corresponding k-mer is removed from the dictionary so that it will not be used in future extensions.

main

public static void main(java.lang.String[] args)

The main method executes the Assembler on a file of sequencing reads. The assembled genome is output to standard out.

Parameters:

args - a String array of any command line arguments