Hi Jan,
Is it possible that the true genotype of the sample that reads were
generated from is actually a mosaic of two (or more) genotypes, and your
subsets happen to be dominated slightly, by random chance, by one or the
other? What happens when you align the reads of each subset to each of the
a
Dear list,
I am trying to use Mauve 2.3.1 to find core- and pan- bacterial genomes, so
I wonder how long it would take to align 48 bacterial genomes, ~ 6 MB each,
on a 64-bit Linux with 4 GB memory using the progressive aligner and
recursive anchor search and looking for LCBs.
Thank you,
Zhao
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Hi Jan,
Based on your description, the issue lies with VelvetOptimiser, not Mauve. The
two read sets resulted in assembly differences which were then detected by
Mauve. My guess is that the assembly differences / rearrangements correlate
with repeats in the genome (rRNA operons, IS elements).
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 rearrangeme
