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]
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