Dear users and moderators,
I am comparing some genomes of different strains of the same bacterium
species. Genomes were sequenced with 454, de novo assembled and are now in
draft format. One of the genomes is a "control" strain. The genomes are to
be compared in the end to this "control" genome.
The questions are:
1. Should I reorder all the drafts against the same reference genome from
NCBI, or should I reorder the "control" strain first, and then reorder the
other strains against the reordered "control" strain (after
concatenating the contigs?)?
2. I am also using ACT to compare the genomes. Perhaps this question should
be sent to a different forum, but I wonder if I should create comparison
files of each genome against the "control" genome or to the external
reference genome from NCBI used during reordering?
Thank you,
SB
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