Hi, In order to get acquainted with Mauve I have generated two different sets of reads from a single set of E. coli WGS data. My expectation was that Progressive Mauve (after applying Contig Mover relative a completed and related genome) should have been able to produce LCBs without rearrangements, since the two sets only differ with respect to quality trimming of the reads. However, using the default settings, Progressive Mauve generates a number of rearrangements and two LCBs in the reverse orientation. By significantly increasing the Min LCB weight (to >180k) I'm able to reduce the number of rearrangements. Nevertheless, one rearrangement persists. Neither does the use of different seeds solve this problem. Similar results are also obtained using the contigs of one set of reads as a reference (in Contig Mover) for the other set of contigs. How do I produce confident alignments of reads originating from different E. coli isolates, given this difficulty in aligning contigs originating from the same sequencing event?
The two sets of reads contained a similar number of paired-end reads (2*945k vs. 2*904k) of high quality scores according to FastQC. VelvetOptimiser produced 146 contigs from the first set of reads (n50 = 169k, longest contig 422k) and 159 contigs from the second set (n50 = 162k, longest contig = 268k). I'm grateful for any input on this matter. Sincerely, Jan Söderman ------------------------------------------------------------------------------ October Webinars: Code for Performance Free Intel webinars can help you accelerate application performance. Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from the latest Intel processors and coprocessors. See abstracts and register > http://pubads.g.doubleclick.net/gampad/clk?id=60134071&iu=/4140/ostg.clktrk _______________________________________________ Mauve-users mailing list Mauve-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/mauve-users
