FlexReseq provides an easily configurable interface to explore resequencing data in a customizable way. Resequencing data consists of a reference sequence and reads from one or more samples that are aligned to that reference sequence. FlexReseq allows the user to step through the reference sequence one position at a time and examine all sample reads that are aligned to that position. The user defines rules about the coverage, quality, paired-end read relationships, and comparisons between samples. These rules are used to pinpoint positions on the reference, such as SNPs, that are of interest to the researcher. Because the user can examine pileups from arbitrarily many samples at once, customized variant types can be easily defined. Additionally, the easily-defined configuration file makes it simple to explore the effect of different parameters when making complex comparisons between two or more resequencing samples.
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