EnglishFrenchSpanish

OnWorks favicon

kissreads - Online in the Cloud

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

This is the command kissreads 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


kissreads - manual page for kissreads 1.2.6

DESCRIPTION


NAME kissReads, version kissreads module 1.2.6 - Copyright INRIA - CeCILL License

SYNOPSIS kissreads/kissreads <toCheck.fasta> <readsC1.fasta> [<readsC2.fasta>
[<readsC3.fasta] ...] [-k value] [-c value] [-d value] [-O value] [-o name] [-u name] [-n]
[-I] [-i index_stride] [-m align_file] [-s] [-f] [-h]

DESCRIPTION Checks for each sequence contained into the toCheck.fasta if it is read
coherent (each position is covered by at least "min_coverage" read(s)) with reads from
readsA.fasta or readsB.fasta A sequence s from toCheck is treated as follow:

if (s coherent with at least one read set): output the sequence as follows

>original fasta comment|C1:min<avg-corr_avg<max|C2:min<avg-cor_avg<max|C3...: >s

With A:min<avg-cor_avg<max standing for : value of the position having minimal
coverage in readsA.fasta < average coverage in readsA.fasta - R-squarred corrected
average in readsA.fa < value of the position having maximal coverage in
readsA.fasta The coverage is the number of reads that perfectly mapped a position
Any other situation (s not coherent with any): couple non read coherent, not
outputed

OPTIONS

-k size_seed: will use seeds of length size_seed. Default: 25.

-O minimal_read_overlap: a read can be mapped if its overlap is a least
"minimal_read_overlap". Default: k

-c min_coverage: a sequence is covered by at least min_coverage coherent reads. Default: 2

-d max_substitutions: Maximal number of substitutions authorized between a read and a
fragment. Note that no substitution is allowed on the central position while
anaylizing the kissnp output. Default: 1.

-o file_name: write read-coherent outputs. Default: standard output

-u file_name: write unread-coherent outputs. Default: standard output

-n the input file (toCheck.fasta) is a kissnp output (incompatible with -I option)

in this case: 1/ only the upper characters are considered (no mapping done on the
extensions) and 2/ the central position (where the SNP occurs) is strictly mapped,
no subsitution is authorized on this position.

-I the input file (toCheck.fasta) is an Intl output (incompatible with -n option)

-i index_stride (int value). This is a heuristic for limiting the memory footprint.
Instead of indexing each kmer of the sequences contained into the toCheck.fasta,
kissreads indexes kmers occurring each "index_stride" position. Default = 1 (no
heuristic)

-t max number of threads (also limited by number of input files)

-m align_file, write a file of reads mapped to sequences in file align_file

-s silent mode

-f outputs coherent events in a standard fasta file format

-h prints this message and exit

Use kissreads online using onworks.net services


Free Servers & Workstations

Download Windows & Linux apps

  • 1
    Avogadro
    Avogadro
    Avogadro is an advanced molecular
    editor designed for cross-platform use
    in computational chemistry, molecular
    modeling, bioinformatics, materials
    science and ...
    Download Avogadro
  • 2
    XMLTV
    XMLTV
    XMLTV is a set of programs to process
    TV (tvguide) listings and help manage
    your TV viewing, storing listings in an
    XML-based format. There are utilities to
    do...
    Download XMLTV
  • 3
    strikr
    strikr
    Strikr Free Software project. Artifacts
    released under a 'intent based'
    dual license: AGPLv3 (community) and
    CC-BY-NC-ND 4.0 international
    (commercial)...
    Download strikr
  • 5
    GIFLIB
    GIFLIB
    giflib is a library for reading and
    writing gif images. It is API and ABI
    compatible with libungif which was in
    wide use while the LZW compression
    algorithm was...
    Download GIFLIB
  • 6
    Alt-F
    Alt-F
    Alt-F provides a free and open source
    alternative firmware for the DLINK
    DNS-320/320L/321/323/325/327L and
    DNR-322L. Alt-F has Samba and NFS;
    supports ext2/3/4...
    Download Alt-F
  • More »

Linux commands

  • 1
    2xml
    2xml
    xml2 - convert xml documents in a flat
    format 2xml - convert flat format into
    xml html2 - convert html documents in a
    flat format 2html - convert flat format
    i...
    Run 2xml
  • 2
    3dldf
    3dldf
    3dldf - a system based on MetaPost for
    creating three-dimensional graphics ...
    Run 3dldf
  • 3
    crashme
    crashme
    crashme - test operating environment
    software robustness ...
    Run crashme
  • 4
    crashstats
    crashstats
    crashstats - Display CrashMail
    statistics ...
    Run crashstats
  • 5
    gbhill
    gbhill
    gbhill - Hill Maximum Likelihhod
    estimation ...
    Run gbhill
  • 6
    gbhisto
    gbhisto
    gbhisto - Produce histogram from data ...
    Run gbhisto
  • More »

Ad