Warning: We consider this version of sff_extract obsolete. The new sff_extract is included now in our tool set seq_crumbs.

sff_extract 0.3.0

sff_extract 0.3.0. Relased on 9-7-2012.

Changes by Bastien Chevreux :

  • fixed bug in clipping points (was an error report by Ion Torrent)

  • reads with partial linkers have “_part” instead of “.part” in the name

  • paired-read naming: .f,.r to /1, /2

  • paired-read: segment not reversed

  • -Q removed, added -A

  • added compat mode “-C”

  • cleaned up usage text

  • run test for ssaha2 before extracting reads

sff_extract 0.2.13

sff_extract 0.2.13. Relased on 27-2-2012.


  • Bugfix by Thuy Nguyen.

sff_extract 0.2.12

sff_extract 0.2.12. Relased on 15-2-2012.


  • Minimun frequency option added by Francisco Pina Martins.

sff_extract 0.2.11

sff_extract 0.2.11. Relased on 13-1-2012.


sff_extract 0.2.10

sff_extract 0.2.10. Relased on 12-9-2011.


  • Bugfix by Bastien.

sff_extract 0.2.8

sff_extract 0.2.8. Relased on 2-3-2010.


  • Bugfix by Bastien. Qualities were not properly reversed when doing paried ends.

sff_extract 0.2.7

sff_extract 0.2.7. Relased on 8-6-2009.


  • Bugfix by Bastien.

sff_extract 0.2.6

sff_extract 0.2.6. Relased on 8-6-2009.


  • Bugfix by Bastien. Fixes a problem with some malformed sff files.

sff_extract 0.2.5

sff_extract 0.2.5. Relased on 6-5-2009.


  • Bugfix release. Paired ends work better now.

sff_extract 0.2.3

sff_extract 0.2.3. Relased on 29-12-2008.


  • Bugfix release. Clipping works again with paired ends and test for ssaha2 removed.

sff_extract 0.2.2

sff_extract 0.2.2. Relased on 30-10-2008.


  • It can work again with python 2.4.

sff_extract 0.2.1

sff_extract 0.2.1. Relased on 13-11-2008.

sff_extract 0.2 represents an important improvement over the 0.1 series. Bastian Chevreux has added support for the paried end sequencing. If you feed sff_extract with a linker sequence you will obtain the paired end sequences split. All the following changes have been coded by Bastien:

  • Reads from paired-end files which are not splitted into 2 sequences now get “.n” postfix.

  • Reads that had mutliple paired-end linkers get “_mlc” in the name and no pairing information written to the XML.

  • sff_extract now return 0 if everything went ok or 1 if there was a problem of any kind.

  • Added left clip plausibility check: check_for_dubious_startseq(). If sequences look fishy, sff_extract prints a warning, continues to extract, but will return with 1 to the shell at the very end.

  • Raises error on empty linker file.

  • Error handling in reading FASTAs

  • Error raised when no SFF file given on command line

  • Fix: XML info now written also for clipped reads (just the clip infor is left out).

  • Added short description of program purpose.

  • Renamed -m to -u and inverted meaning: lowercasing clipped parts is now default.

  • Added –min_left_clip.

  • Added –version.

sff_extract 0.1.2

sff_extract 0.1.2. Relased on 30-10-2008.


  • It can work again with python 2.4.

sff_extract 0.1.1

sff_extract 0.1.1. Relased on 16-10-2008.


  • “o” option added to specify a common basename for all output files.

  • More simple error messages thrown.

sff_extract 0.1

sff_extract 0.1. Relased on 14-10-2008.


  • Initial Release. Save the script, make it executable and run it.