EnglishFrenchSpanish

Ad


OnWorks favicon

bowtie-build - Online in the Cloud

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

This is the command bowtie-build 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


bowtie-build - building a colorspace index for bowtie

SYNOPSIS


bowtie-build [options]* <reference_in> <ebwt_outfile_base>

DESCRIPTION


reference_in
comma-separated list of files with ref sequences

ebwt_outfile_base
write Ebwt data to files with this dir/basename

OPTIONS


-f reference files are Fasta (default)

-c reference sequences given on cmd line (as <seq_in>)

--large-index
force generated index to be 'large', even if ref has fewer than 4 billion
nucleotides

-C/--color
build a colorspace index

-a/--noauto
disable automatic -p/--bmax/--dcv memory-fitting

-p/--packed
use packed strings internally; slower, uses less mem

--bmax <int>
max bucket sz for blockwise suffix-array builder

--bmaxdivn <int>
max bucket sz as divisor of ref len (default: 4)

--dcv <int>
diff-cover period for blockwise (default: 1024)

--nodc disable diff-cover (algorithm becomes quadratic)

-r/--noref
don't build .3/.4.ebwt (packed reference) portion

-3/--justref
just build .3/.4.ebwt (packed reference) portion

-o/--offrate <int>
SA is sampled every 2^offRate BWT chars (default: 5)

-t/--ftabchars <int>
# of chars consumed in initial lookup (default: 10)

--ntoa convert Ns in reference to As

--seed <int>
seed for random number generator

-q/--quiet
verbose output (for debugging)

-h/--help
print detailed description of tool and its options

--usage
print this usage message

--version
print version information and quit

64-bit Built on lgw01-11 Thu Nov 26 11:11:03 UTC 2015 Compiler: gcc version 5.2.1 20151123
(Ubuntu 5.2.1-25ubuntu1) Options: -O3 -Wl,--hash-style=both -D_FORTIFY_SOURCE=2 -g -O2
-fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fstack-protector-strong
-Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro Sizeof {int, long,
long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}

Use bowtie-build online using onworks.net services


Free Servers & Workstations

Download Windows & Linux apps

  • 1
    oStorybook
    oStorybook
    oStorybook l'outil privil�gi� des
    �crivains. ATTENTION : voir sur
    http://ostorybook.tuxfamily.org/v5/
    --en_EN oStorybook the right tool for
    writers. WARNIN...
    Download oStorybook
  • 2
    Asuswrt-Merlin
    Asuswrt-Merlin
    Asuswrt-Merlin is a third party
    firmware for select Asus wireless
    routers. Based on the Asuswrt firmware
    developed by Asus, it brings tweaks, new
    features and ...
    Download Asuswrt-Merlin
  • 3
    Atom
    Atom
    Atom is a text editor that's
    modern, approachable and full-featured.
    It's also easily customizable- you
    can customize it to do anything and be
    able to ...
    Download Atom
  • 4
    Osu!
    Osu!
    Osu! is a simple rhythm game with a well
    thought out learning curve for players
    of all skill levels. One of the great
    aspects of Osu! is that it is
    community-dr...
    Download Osu!
  • 5
    LIBPNG: PNG reference library
    LIBPNG: PNG reference library
    Reference library for supporting the
    Portable Network Graphics (PNG) format.
    Audience: Developers. Programming
    Language: C. This is an application that
    can also...
    Download LIBPNG: PNG reference library
  • 6
    Metal detector based on  RP2040
    Metal detector based on RP2040
    Based on Raspberry Pi Pico board, this
    metal detector is included in pulse
    induction metal detectors category, with
    well known advantages and disadvantages.
    RP...
    Download Metal detector based on RP2040
  • More »

Linux commands

Ad