EnglishFrenchSpanish

OnWorks favicon

sak - Online in the Cloud

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

This is the command sak 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


sak - Slicing and dicing of FASTA/FASTQ files..

SYNOPSIS

sak [OPTIONS] [\B-o OUT.{fa,fq}] IN.{fa,fq}

DESCRIPTION

"It slices, it dices and it makes the laundry!"

Rewrite of the original SAK tool by Manuel Holtgrewe.

-h, --help

Displays this help message.

--version

Display version information

Output Options:

-o, --out-path FASTX

Path to the resulting file. If omitted, result is printed to stdout. Use files
ending in .fq or . to write out FASTQ. Valid filetypes are: .fq, .fastq, .fa,
.fasta, .faa, .ffn, .fna, and .frn.

-rc, --revcomp

Reverse-complement output.

-l, --max-length LEN

Maximal number of sequence characters to write out.

Filter Options:

-s, --sequence NUM

Select the given sequence for extraction by 0-based index.

-sn, --sequence-name NAME

Select sequence with name prefix being NAME.

-ss, --sequences RANGE

Select sequences from-to where from and to are 0-based indices.

-i, --infix RANGE

Select characters from-to where from and to are 0-based indices.

-ll, --line-length LEN

Set line length in output file. See section Line Length for details. In range
[-1..inf].

LINE LENGTH

You can use the setting --line-length for setting the resulting line length. By
default, sequences in FASTA files are written with at most 70 characters per line
and sequences in FASTQ files are written without any line breaks. The quality
sequence in FASTQ file is written in the same way as the residue sequence.

The default is selected with a --line-length value of -1 and line breaks can be
disabled with a value of 0.

USAGE EXAMPLES

sak -s 10 IN.fa

Cut out 11th sequence from IN.fa and write to stdout as FASTA.

sak -ss 10-12 -ss 100-200 IN.fq

Cut out 11th up to and including 12th and 101th up to and including 199th sequence
from IN.fq and write to stdout as FASTA.

VERSION

sak version: 0.2 Last update November 2012

Use sak online using onworks.net services


Free Servers & Workstations

Download Windows & Linux apps

  • 1
    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
  • 2
    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
  • 3
    Xtreme Download Manager
    Xtreme Download Manager
    The project has a new home now:
    https://xtremedownloadmanager.com/ For
    developers:
    https://github.com/subhra74/xdm Xtreme
    Download Manager is a powerful tool t...
    Download Xtreme Download Manager
  • 4
    TTGO VGA32 Lite
    TTGO VGA32 Lite
    Features:4:3 and 16:9 low resolution
    VGA outputPS/2 keyboard and mouse
    inputText-based user interface (TUI)
    with dialog managerPartial Unicode
    supportSlave dis...
    Download TTGO VGA32 Lite
  • 5
    Clover EFI bootloader
    Clover EFI bootloader
    Project has moved to
    https://github.com/CloverHackyColor/CloverBootloader..
    Features:Boot macOS, Windows, and Linux
    in UEFI or legacy mode on Mac or PC with
    UE...
    Download Clover EFI bootloader
  • 6
    unitedrpms
    unitedrpms
    Join us in Gitter!
    https://gitter.im/unitedrpms-people/Lobby
    Enable the URPMS repository in your
    system -
    https://github.com/UnitedRPMs/unitedrpms.github.io/bl...
    Download unitedrpms
  • More »

Linux commands

Ad