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This is the command HPCmapper 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



HPCmapper - generate a script to map reads


HPCmapper [-vb] [-kint(20)] [-wint(6)] [-hint(50)] [-tint] [-Mint]
[-edouble(.85)][-lint(1000)] [-sint(100)] [-Hint] [-mtrack]+ [-dalint(4)] [-degint(25)]
ref:db|dam reads:db|dam [first:int[-last:int]]


HPCmapper writes a UNIX shell script to the standard output that consists of a sequence of
commands that effectively "maps" every read in the DB reads against a reference set of
sequences in the DB ref, recording all the found local alignments in the sequence of files
ref.reads.1.las, ref.reads.2.las, and so on, where ref.reads.k.las contains the alignments
between all of ref and the k'th block of reads. The parameters are exactly the same as
for HPCdaligner(1) save that the -k, -h, and -e defaults are set appropriately for
mapping, and the -A and -I options make no sense as ref and reads are expected to be
distinct data sets.

If the integers first and last are missing, then the script produced is for every block in
the database reads. If first is present then HPCmapper produces an script that compares
blocks first through last (last = first if not present) against DAM ref.

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