AlphaSeqOpt is a software package for determining the optimum distribution of sequencing resources within a population of interest. AlphaSeqOpt determines which individuals should be prioritised for sequencing and the total investment to be made in sequencing this individual. The aim of the algorithm is to capture, sequence and phase as many of the population haplotypes as possible for maximum sequence imputation ability into the rest of the population.
There are two different methods implemented in AlphaSeqOpt:
Method 1 – Selects the top n individuals that carry more of the most frequent haplotypes in the population and optimises the distribution of a fixed sequencing budget across them and their families to enable phasing of their haplotypes at the sequence level.
Method 2 – Determines which individuals should be prioritised for sequencing and the total investment to be made in sequencing these individuals so that the maximum number of haplotypes in the population are sequenced at a target coverage that is high enough to derive highly accurate consensus haplotypes used for whole-population imputation of low-coverage sequence data.
1. User Manual
The manual can be viewed here.
2. Binaries for Linux, Mac and Windows
The AlphaSeqOpt1.1 folder contains:
- 1 program executable (AlphaSeqOpt)
- 1 manual in pdf format (AlphaSeqOpt User Manual)
- 1 parameter file template (AlphaSeqOptSpec.txt)
- 2 folders containing examples
Running AlphaSeqOpt requires AlphaSeqOptSpec.txt and the user’s input files. The required input files differ for each of the two methods implemented in AlphaSeqOpt. Further details are given in the user manual.
Examples of both methods implemented in AlphaSeqOpt1.1.1. The folder TestDataASO1 contains all the input files required to run method 1 of AlphaSeqOpt and the output files generated. The folder TestDataASO2 contains all the input files required to run method 2 of AlphaSeqOpt and the output files generated.
Mac OS: Download