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LAshow - Online in the Cloud

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This is the command LAshow that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator



LAshow - display local alignments from .las files


LAshow [-caroUF] [-iint(4)] [-wint(100)][-bint(10)] src1:db|dam [src2:db|dam] align:las
[reads:FILE | reads:range ... ]


LAshow produces a printed listing of the local alignments contained in the specified .las
file, where the a- and b-reads come from src1 or from src1 and src2, respectively. If a
file or list of read ranges is given, then only the overlaps for which the a-read is in
the set specified by the file or list are displayed. See DBshow(1) for an explanation of
how the file and list of read ranges are interpreted.


-F Reverse the roles of the a- and b- reads in the display

-U Use uppercase for DNA sequence instead of the default lowercase

Set the indent for the cartoon and/or alignment displays if they are requested.
(default: 4)

Set the number of symbols on either side of the aligned segments in an alignment
display. (default: 10)

-ww This parameter is used for the display modes specified by -a and -r. (default:

-o Only display alignments that are proper overlaps-- that is, where a sequence end
occurs at each end of the alignment

-c Cartoon rendering of the alignment

-a, -r Display an alignment of the local alignment

The -a option puts exactly w columns per segment of the display, whereas the -r option
puts exactly w a-read symbols in each segment of the display. The -r display mode is
useful when one wants to visually compare two alignments involving the same a-read. If a
combination of the -c, -a, and -r flags is set, then the cartoon comes first, then the -a
alignment, and lastly the -r alignment.

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