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]

FILES¶

adaptors.fasta: Provide contaminant sequences as a fasta-formatted file.


                 See ´/usr/share/doc/scythe/illumina_adaptors.fa´.


                 N.B.: Index/Barcode sequences should be substituted for Ns in


                 the example adaptor file.

AUTHOR¶

Vince Buffalo, https://github.com/vsbuffalo