3,481
edits
Changes
→nucmer: standardizing the way the options are layed out
but not necessarily unique in the query (default behavior)
--maxmatch Use all anchor matches regardless of their uniqueness
-b|breaklen Set the distance an alignment extension will attempt to
extend poor scoring regions before giving up (default 200)
(default 0.12)
--[no]extend Toggle the cluster extension step (default --extend)
-f --|forward Use only the forward strand of the Query sequences
-g|maxgap Set the maximum gap between two adjacent matches in a
cluster (default 90)
-h --|help Display help information and exit
-l|minmatch Set the minimum length of a single match (default 20)
-o --|coords Automatically generate the original NUCmer1.1 coords
output file using the 'show-coords' program
--[no]optimize Toggle alignment score optimization, i.e. if an alignment
alignment at the end of the sequence (default --optimize)
-p|prefix Set the prefix of the output files (default "out")
-r --|reverse Use only the reverse complement of the Query sequences
--[no]simplify Simplify alignments by removing shadowed clusters. Turn
this option off if aligning a sequence to itself to look
for repeats (default --simplify)
-V --|version Display the version information and exit
</pre>