EnglishFrenchSpanish

Ad


OnWorks favicon

fastaq - Online in the Cloud

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

This is the command fastaq 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


fastaq - FASTA and FASTQ file manipulation tools

SYNOPSIS


fastaq <command> [options]

DESCRIPTION0nf


To get minimal usage for a command use: fastaq command

To get full help for a command use one of: fastaq command -h fastaq command --help

Available commands:

add_indels Deletes or inserts bases at given position(s) caf_to_fastq
Converts a CAF file to FASTQ format capillary_to_pairs Converts file of capillary
reads to paired and unpaired files chunker Splits sequences into equal
sized chunks count_sequences Counts the sequences in input file deinterleave
Splits interleaved paired file into two separate files enumerate_names Renames
sequences in a file, calling them 1,2,3... etc expand_nucleotides Makes every
combination of degenerate nucleotides fasta_to_fastq Convert FASTA and .qual to
FASTQ filter Filter sequences to get a subset of them get_ids
Get the ID of each sequence get_seq_flanking_gaps Gets the sequences flanking gaps
interleave Interleaves two files, output is alternating between fwd/rev reads
make_random_contigs Make contigs of random sequence merge Converts
multi sequence file to a single sequence replace_bases Replaces all occurrences
of one letter with another reverse_complement Reverse complement all sequences
scaffolds_to_contigs Creates a file of contigs from a file of scaffolds search_for_seq
Find all exact matches to a string (and its reverse complement) sequence_trim
Trim exact matches to a given string off the start of every sequence sort_by_size
Sorts sequences in length order split_by_base_count Split multi sequence file into
separate files strip_illumina_suffix Strips /1 or /2 off the end of every read name
to_boulderio Converts to Boulder-IO format, used by primer3 to_fake_qual
Make fake quality scores file to_fasta Converts a variety of input formats
to nicely formatted FASTA format to_mira_xml Create an xml file from a file of
reads, for use with Mira assembler to_orfs_gff Writes a GFF file of open
reading frames to_perfect_reads Make perfect paired reads from reference
to_random_subset Make a random sample of sequences (and optionally mates as well)
to_tiling_bam Make a BAM file of reads uniformly spread across the input
reference to_unique_by_id Remove duplicate sequences, based on their names. Keep
longest seqs translate Translate all sequences in input nucleotide sequences
trim_Ns_at_end Trims all Ns at the start/end of all sequences trim_contigs
Trims a set number of bases off the end of every contig trim_ends Trim fixed
number of bases of start and/or end of every sequence version Print version
number and exit

Use fastaq online using onworks.net services


Free Servers & Workstations

Download Windows & Linux apps

  • 1
    OpenFOAM
    OpenFOAM
    OpenFOAM - The Open Source CFD Toolbox.
    OpenFOAM is a generic, programmable
    software tool for Computational Fluid
    Dynamics (CFD). For more information,
    see: - ...
    Download OpenFOAM
  • 2
    PostInstallerF
    PostInstallerF
    PostInstallerF will install all the
    software that Fedora Linux and others
    doesn't include by default, after
    running Fedora for the first time. Its
    easy for...
    Download PostInstallerF
  • 3
    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
  • 4
    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
  • 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
  • 7
    Old Feren OS Repositories
    Old Feren OS Repositories
    This was the Official Repository for
    Feren OS. To add the latest one, run
    this command: (16.04-based) echo
    "deb ...
    Download Old Feren OS Repositories
  • More »

Linux commands

Ad