MOTIVATION: Pooling multiple samples increases the efficiency and lowers the cost of DNA sequencing. One approach to multiplexing is to use short DNA indices to uniquely identify each sample. After sequencing, reads must be assigned in silico to the sample of origin, a process referred to as demultiplexing. Demultiplexing software typically identifies the sample of origin using a fixed number of mismatches between the read index and a reference index set. This approach may fail or misassign reads when the sequencing quality of the indices is poor. RESULTS: We introduce deML, a maximum likelihood algorithm that demultiplexes Illumina sequences. deML computes the likelihood of an observed index sequence being derived from a specified sample. A quality score which reflects the probability of the assignment being correct is generated for each read. Using these quality scores, even very problematic datasets can be demultiplexed and an error threshold can be set. AVAILABILITY AND IMPLEMENTATION: deML is freely available for use under the GPL (http://bioinf.eva.mpg.de/deml/).

In order to shed light on the rate and mode of evolution of DNA sequence evolution in the germ line of humans and chimpanzees, we have sequenced 136 kb around the human ZFY gene as well as a total of 180 kb of genomic DNA surrounding the ZFX and ZFY genes on the chimpanzee X and Y chromosome, respectively. The comparison of the orthologous sequences on the human and chimpanzee sex chromosomes show that whereas the ZFX region display 0.8% substitutional differences between the two species, the ZFY region display 1.5% differences. By contrast, insertions and deletions show no difference between the two regions. Interestingly, transversions show a much more drastic preponderance in the male germ line than transitions, and the insertion of retroviral-like elements seem to occur more frequently in the male than in the female germ line.