OnWorks favicon

HPCmapper - Online in the Cloud

Run HPCmapper in OnWorks free hosting provider over Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

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.

Use HPCmapper online using onworks.net services

Free Servers & Workstations

Download Windows & Linux apps

  • 1
    Modular headtracking program that
    supports multiple face-trackers, filters
    and game-protocols. Among the trackers
    are the SM FaceAPI, AIC Inertial Head
    Tracker ...
    Download facetracknoir
  • 2
    PHP QR Code
    PHP QR Code
    PHP QR Code is open source (LGPL)
    library for generating QR Code,
    2-dimensional barcode. Based on
    libqrencode C library, provides API for
    creating QR Code barc...
    Download PHP QR Code
  • 3
    Freeciv is a free turn-based
    multiplayer strategy game, in which each
    player becomes the leader of a
    civilization, fighting to obtain the
    ultimate goal: to bec...
    Download Freeciv
  • 4
    Cuckoo Sandbox
    Cuckoo Sandbox
    Cuckoo Sandbox uses components to
    monitor the behavior of malware in a
    Sandbox environment; isolated from the
    rest of the system. It offers automated
    analysis o...
    Download Cuckoo Sandbox
  • 5
    Play YouTube video on LMS (porting of
    Triode's to YouTbe API v3) This is
    an application that can also be fetched
    Download LMS-YouTube
  • 6
    Windows Presentation Foundation
    Windows Presentation Foundation
    Windows Presentation Foundation (WPF)
    is a UI framework for building Windows
    desktop applications. WPF supports a
    broad set of application development
    Download Windows Presentation Foundation
  • More »

Linux commands