EnglishFrenchSpanish

Ad


OnWorks favicon

HPCdaligner - Online in the Cloud

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

This is the command HPCdaligner 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

PROGRAM:

NAME


HPCdaligner - generate a script to run daligner(1)

SYNOPSIS


HPCdaligner [-vbAI] [-kint(14)] [-wint(6)][-hint(35)] [-tint] [-Mint] [-edouble(.70)]
[-lint(1000)] [-sint(100)] [-Hint] [-mtrack]+ [-dalint(4)] [-degint(25)] path:db|dam
[first:int[-last:int]]

DESCRIPTION


HPCdaligner writes a UNIX shell script to the standard output that consists of a sequence
of commands that effectively run daligner(1) on all pairs of blocks of a split database
and then externally sorts and merges them using LAsort(1) and LAmerge(1) into a collection
of alignment files with names path.#.las where # ranges from 1 to the number of blocks the
database is split into. These sorted files if concatenated by say LAcat(1) would contain
all the alignments in sorted order (of a-read, then b-read, and so on). Moreover, all
overlaps for a given a-read are guaranteed to not be split across files, so one can run
artifact analyzers or error correction on each sorted file in parallel.

The database must have been previously split by DBsplit(1) and all the parameters, except
-v, -dal, and -deg, are passed through to the calls to daligner(1). The defaults for
these parameters are as for daligner(1). The -v flag, for verbose-mode, is also passed to
all calls to LAsort(1) and LAmerge(1). -dal and -deg options are described later.

For a database divided into N sub-blocks, the calls to daligner(1) will produce in total
2TN^2 .las files assuming daligner runs with T threads. These will then be sorted and
merged into N^2 sorted .las files, one for each block pair. These are then merged in
ceil(log_deg N) phases where the number of files decreases geometrically in -deg until
there is 1 file per row of the N x N block matrix. So at the end one has N sorted .las
files that when concatenated would give a single large sorted overlap file.

The -dal option (default 4) gives the desired number of block comparisons per call to
daligner(1). Some must contain dal-1 comparisons, and the first dal-2 block comparisons
even less, but the HPCdaligner "planner" does the best it can to give an average load of
dal block comparisons per command. The -deg option (default 25) gives the maximum number
of files that will be merged in a single LAmerge(1) command. The planner makes the most
even k-ary tree of merges, where the number of levels is ceil(log_deg N).

If the integers first and last are missing, then the script produced is for every block in
the database. If first is present, then HPCdaligner produces an incremental script that
compares blocks first through last (last = first if not present) against each other and
all previous blocks 1 through first-1, and then incrementally updates the .las files for
blocks 1 through first-1, and creates the .las files for blocks first through last.

Each UNIX command line output by the HPCdaligner can be a batch job (we use the &&
operator to combine several commands into one line to make this so). Dependencies between
jobs can be maintained simply by first running all the daligner(1) jobs, then all the
initial sort jobs, and then all the jobs in each phase of the external merge sort. Each
of these phases is separated by an informative comment line for your scripting
convenience.

Use HPCdaligner online using onworks.net services


Free Servers & Workstations

Download Windows & Linux apps

  • 1
    AstrOrzPlayer
    AstrOrzPlayer
    AstrOrz Player is a free media player
    software, part based on WMP and VLC. The
    player is in a minimalist style, with
    more than ten theme colors, and can also
    b...
    Download AstrOrzPlayer
  • 2
    movistartv
    movistartv
    Kodi Movistar+ TV es un ADDON para XBMC/
    Kodi que permite disponer de un
    decodificador de los servicios IPTV de
    Movistar integrado en uno de los
    mediacenters ma...
    Download movistartv
  • 3
    Code::Blocks
    Code::Blocks
    Code::Blocks is a free, open-source,
    cross-platform C, C++ and Fortran IDE
    built to meet the most demanding needs
    of its users. It is designed to be very
    extens...
    Download Code::Blocks
  • 4
    Amidst
    Amidst
    Amidst or Advanced Minecraft Interface
    and Data/Structure Tracking is a tool to
    display an overview of a Minecraft
    world, without actually creating it. It
    can ...
    Download Amidst
  • 5
    MSYS2
    MSYS2
    MSYS2 is a collection of tools and
    libraries providing you with an
    easy-to-use environment for building,
    installing and running native Windows
    software. It con...
    Download MSYS2
  • 6
    libjpeg-turbo
    libjpeg-turbo
    libjpeg-turbo is a JPEG image codec
    that uses SIMD instructions (MMX, SSE2,
    NEON, AltiVec) to accelerate baseline
    JPEG compression and decompression on
    x86, x8...
    Download libjpeg-turbo
  • More »

Linux commands

  • 1
    abi-tracker
    abi-tracker
    abi-tracker - visualize ABI changes
    timeline of a C/C++ software library.
    DESCRIPTION: NAME: ABI Tracker
    (abi-tracker) Visualize ABI changes
    timeline of a C/C+...
    Run abi-tracker
  • 2
    abicheck
    abicheck
    abicheck - check application binaries
    for calls to private or evolving symbols
    in libraries and for static linking of
    some system libraries. ...
    Run abicheck
  • 3
    couriermlm
    couriermlm
    couriermlm - The Courier mailing list
    manager ...
    Run couriermlm
  • 4
    couriertcpd
    couriertcpd
    couriertcpd - the Courier mail server
    TCP server daemon ...
    Run couriertcpd
  • 5
    gbklatex
    gbklatex
    bg5latex - Use LaTeX directly on a Big5
    encodedtex file bg5pdflatex - Use
    pdfLaTeX directly on a Big5 encodedtex
    file bg5+latex - Use LaTeX directly on a
    Big5+...
    Run gbklatex
  • 6
    gbkpdflatex
    gbkpdflatex
    bg5latex - Use LaTeX directly on a Big5
    encodedtex file bg5pdflatex - Use
    pdfLaTeX directly on a Big5 encodedtex
    file bg5+latex - Use LaTeX directly on a
    Big5+...
    Run gbkpdflatex
  • More »

Ad