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Sffinfo

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The sffinfo command extract sequences reads from a .sff file.



Default settings

The sffinfo command requires that the user provide a .sff or sff.txt file. You may enter multiple sff files by separating them by -'s. For example: F5MMO9001.sff-GHL4YHV01.sff.

mothur > sffinfo(sff=F5MMO9001.sff)

This command will generate two files - F5MMO9001.fasta and F5MMO9001.qual. By default these are the trimmed.

or to parse a sff.txt file:

mothur > sffinfo(sfftxt=F5MMO9001.sff.txt)

This command will generate two files - F5MMO9001.sff.fasta and F5MMO9001.sff.qual. By default these are the trimmed.

Options

fasta

The fasta parameter allows you to indicate if you would like a fasta file generated. By default fasta=True.

 mothur > sffinfo(sff=F5MMO9001.sff, fasta=F)

qfile

The qfile parameter allows you to indicate if you would like a quality file generated. By default qfile=True.

 mothur > sffinfo(sff=F5MMO9001.sff, qfile=F)

trim

The trim parameter allows you to indicate if you would like a sequences and quality scores trimmed to the clipQualLeft and clipQualRight values. By default trim=True, but you can extract the raw sequence data by setting trim=false.

 mothur > sffinfo(sff=F5MMO9001.sff, trim=f)

sfftxt

The sfftxt parameter allows you to indicate if you would like a sff.txt file generated. By default sfftxt=false.

 mothur > sffinfo(sff=F5MMO9001.sff, sfftxt=T)

flow

The flow parameter allows you to indicate if you would like a flowgram file generated. By default flow=true.

 mothur > sffinfo(sff=F5MMO9001.sff, flow=T)

accnos

The accnos parameter allows you to provide a accnos file containing the names of the sequences you would like extracted. You may enter multiple files by separating them by -'s.

 mothur > sffinfo(sff=F5MMO9001.sff, accnos=F5MMO9001.accnos)

oligos

The oligos option takes a file that can contain the sequences of the forward and reverse primers and barcodes and their sample identifier. Each line of the oligos file can start with the key words "forward", "reverse", "barcode", "linker" and "spacer" or it can start with a "#" to tell mothur to ignore that line of the oligos file. For example, consider a trimmed version of F5MMO9001.oligos:

forward	ATTACCGCGGCTGCTGG	v13
forward	CCGTCAATTCMTTTRAGT	v35
forward	TACGGYTACCTTGTTAYGACTT	v69
barcode	TCACCTC	F5MMO9001.700015271.WUGSC
barcode	TGCGTTC	F5MMO9001.700015280.WUGSC
barcode	ACGGCTC	F5MMO9001.700015283.WUGSC
barcode	TATTGAC	F5MMO9001.700015656.WUGSC
barcode	TAATCTC	F5MMO9001.700015677.WUGSC
...

bdiffs & pdiffs & ldiffs & sdiffs & tdiffs

These parameters are used to allow differences in the barcode, primers, linkers and spacers. pdiffs is maximum number of differences to the primer sequence, default=0. bdiffs is maximum number of differences to the barcode sequence, default=0. ldiffs is maximum number of differences to the linker sequence, default=0. sdiffs is maximum number of differences to the spacer sequence, default=0. tdiffs is maximum total number of differences to the barcode, primer, linker and spacer (default to pdiffs + bdiffs + ldiffs + sdiffs).

Revisions

  • 1.24.0 - flow default changed to true, added a warning about corrupted sff files.
  • 1.28.0 - added oligos, pdiffs, sdiffs, ldiffs, bdiffs and tdiffs options.
  • 1.30.0 - Bug fix: trimmed the entire sequence if clipQualRight=0.
  • 1.33.0 - Added the group parameter.
  • 1.33.0 - Bug Fix: Windows version with oligos file caused corrupt sff files after parse. - [1]
  • 1.36.0 - Bug Fix: Off by one in right side trimming. http://www.mothur.org/forum/viewtopic.php?f=4&t=3764