SYNOPSIS

DESCRIPTION

-1

1-to-1 alignment allowing for rearrangements (intersection of -r and -q alignments)

-g

1-to-1 global alignment not allowing rearrangements

-h

Display help information

-i float

Set the minimum alignment identity [0, 100], default 0

-l int

Set the minimum alignment length, default 0

-m

Many-to-many alignment allowing for rearrangements (union of -r and -q alignments)

-q

Maps each position of each query to its best hit in the reference, allowing for reference overlaps

-r

Maps each position of each reference to its best hit in the query, allowing for query overlaps

-u float Set the minimum alignment uniqueness, i.e. percent of

the alignment matching to unique reference AND query sequence [0, 100], default 0

-o float

Set the maximum alignment overlap for -r and -q options as a percent of the alignment length [0, 100], default 100

-v

Print the discarded alignments instead of those that pass filters

-b

Maps duplications (XOR of -r and -q alignments, one or the other but not both)

Reads a delta alignment file from either nucmer or promer and filters the alignments based on the command-line switches, leaving only the desired alignments which are output to stdout in the same delta format as the input. For multiple switches, order of operations is as follows: -i -l -u -q -r -g -m -1 -b. If an alignment is excluded by a preceding operation, it will be ignored by the succeeding operations.

An important distinction between the -g option and the -1 and -m options is that -g requires the alignments to be mutually consistent in their order, while the -1 and -m options are not required to be mutually consistent and therefore tolerate translocations, inversions, etc. In general cases, the -m option is the best choice, however -1 can be handy for applications such as SNP finding which require a 1-to-1 mapping. Finally, for mapping query contigs, or sequencing reads, to a reference genome, use -q. The duplications printed with the -b option are -r and -q alignments that are not present in the 1-to-1 alignment. These alignments are also the difference between the -1 and -m alignments