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2015

Optimal Haplotype Assembly from High-Throughput Mate-Pair Reads

Kamath, Govinda M., Şaşoğlu, Eren, Tse, David

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Understand

Humans have $23$ pairs of homologous chromosomes.

The homologous pairs are almost identical pairs of chromosomes.
For the most part, differences in homologous chromosome occur at certain documented positions called single nucleotide polymorphisms (SNPs).
A haplotype of an individual is the pair of sequences of SNPs on the two homologous chromosomes.

Optimal Haplotype Assembly from High-Throughput Mate-Pair Reads · Around

Built on

Convolutional codes and their performance in communication systems
Original
Andrew J Viterbi · 1971
Earlier work this paper cites.
Optimal algorithms for haplotype assembly from whole-genome sequence data
Dan He, Arthur Choi, Knot Pipatsrisawat, Adnan Darwiche, and Eleazar Eskin · 2010
Earlier work this paper cites.
Haplotype phasing: existing methods and new developments
Sharon R Browning and Brian L Browning · 2011
Earlier work this paper cites.

Similar

Available at http://www.illumina.com/documents/products/technotes/technote_nextera%_matepair_data_processing.pdf
Data Processing of Nextera Mate Pair Reads on Illumina Sequencing Platforms, · 2012
Cited alongside, same era.
Elements of information theory
Thomas M Cover and Joy A Thomas · 2012
Cited alongside, same era.

Then

The Database of Short Genetic Variation (dbSNP)
Adrienne Kitts, Lon Phan, Minghong Ward, and John Bradley Holmes · 2014
Later among the works it cites.
Haplotype Assembly: An Information Theoretic View
Original
Hongbo Si, Haris Vikalo, and Sriram Vishwanath · 2014
Later among the works it cites.

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