Test read data from the 454 Life Sciences platform can be downloaded here. The data within the zipped file is from patient D from a study looking at co-receptor variation through time. Further details of this study are available [PLoS Comput Biol. 2010 Dec 16;6(12):e1001022]. For test purposes the template provided within the zip file is that of the envelope region of HXB2.

H1N1 read data generated on both the 454 Life Sciences and Illumina platforms, as described in our submitted manuscript, is available here.

1. Bayesian Polymorphism Detection: Given temporally sampled data, early time points can be used to obtain priors that can subsequently be used, in conjunction with later time points, to obtain posterior probabilities on polymorphic characters within the assembly.
2. Separate k-mer mapping and pairwise alignments as well as allowing for mapping to multiple templates: For many studies the k-mer mapping of reads to a template is sufficient and the subsequent slower pairwise alignment step is redundant. Examples include (a) mapping reads to multiple reference sequences in relation to pairwise competition assays where coverage is proportional to fitness, (b) given a set of reference sequences the determination breakpoint locations with the viral population between these sequences using cover and (c) metagenomics where a database of reference sequences is available and reads can be mapped to the database.
3. Recombination detection: Both using current recombination detection algorithms on short read data as well as using coverage in conjunction to a set of reference sequences in order to detect breakpoints.