EnglishFrenchSpanish

OnWorks favicon

scythe - Online in the Cloud

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

This is the command scythe 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


scythe - Bayesian adaptor trimmer

SYNOPSIS


scythe -t sanger -a /path/to/adaptors.fasta [options] <sequences.fastq.gz>

Trim 3´-end adaptor contaminants off sequence files. If no output file is specified,
scythe will use stdout.

OPTIONS


-p, --prior prior (default: 0.300)
-q, --quality-type quality type, either illumina, solexa, or sanger (default: sanger)
-m, --matches-file matches file (default: no output)
-o, --output-file output trimmed sequences file (default: stdout)
-t, --tag add a tag to the header indicating Scythe cut a sequence (default: off)
-n, --min-match smallest contaminant to consider (default: 5)
-M, --min-keep filter sequences less than or equal to this length (default: 35)
--quiet don´t output statistics about trimming to stdout (default: off)
--help display this help and exit
--version output version information and exit

These are the quality encoding schemes scythe recognises (see ´--quality´)

phred PHRED quality scores (e.g. from Roche 454). ASCII with no
offset, range: [4, 60].
sanger Sanger are PHRED ASCII qualities with an offset of 33,
range: [0, 93]. From NCBI SRA, or Illumina pipeline 1.8+.
solexa Solexa (also very early Illumina -- pipeline < 1.3).
ASCII offset of 64, range: [-5, 62]. Uses a different
quality-to-probabilities conversion than other schemes.
illumina Illumina output from pipeline versions between 1.3 and 1.7.
ASCII offset of 64, range: [0, 62]

Use scythe online using onworks.net services


Free Servers & Workstations

Download Windows & Linux apps

  • 1
    strace
    strace
    The strace project has been moved to
    https://strace.io. strace is a
    diagnostic, debugging and instructional
    userspace tracer for Linux. It is used
    to monitor a...
    Download strace
  • 2
    gMKVExtractGUI
    gMKVExtractGUI
    A GUI for mkvextract utility (part of
    MKVToolNix) which incorporates most (if
    not all) functionality of mkvextract and
    mkvinfo utilities. Written in C#NET 4.0,...
    Download gMKVExtractGUI
  • 3
    JasperReports Library
    JasperReports Library
    JasperReports Library is the
    world's most popular open source
    business intelligence and reporting
    engine. It is entirely written in Java
    and it is able to ...
    Download JasperReports Library
  • 4
    Frappe Books
    Frappe Books
    Frappe Books is a free and open source
    desktop book-keeping software that's
    simple and well-designed to be used by
    small businesses and freelancers. It'...
    Download Frappe Books
  • 5
    Numerical Python
    Numerical Python
    NEWS: NumPy 1.11.2 is the last release
    that will be made on sourceforge. Wheels
    for Windows, Mac, and Linux as well as
    archived source distributions can be fou...
    Download Numerical Python
  • 6
    CMU Sphinx
    CMU Sphinx
    CMUSphinx is a speaker-independent large
    vocabulary continuous speech recognizer
    released under BSD style license. It is
    also a collection of open source tools ...
    Download CMU Sphinx
  • More »

Linux commands

crm
crm
Use crm online using onworks.net
services. ...
Run crm
  • 4
    crmgr
    crmgr
    crmgr - administration utility for QDBM
    Curia ...
    Run crmgr
  • 5
    gappletviewer
    gappletviewer
    gappletviewer - Load and runs an applet
    ...
    Run gappletviewer
  • 6
    gaps
    gaps
    mummer - package for sequence alignment
    of multiple genomes ...
    Run gaps
  • s-processed="true">
    g15stats
    g15stats - A CPU/Memory/Swap usage
    meter for G15Daemon DESCRIPTION: The
    packages provides the following usage
    meter for LCD on some Logitech
    keyboards, usind g...
    Run g15stats
  • More »
  • Ad