NAME

       ssake - assembling millions of very short DNA sequences

SYNOPSIS

       Progressive  assembly  of  millions  of  short DNA sequences by k-mer search through a prefix tree and 3'
       extension.

OPTIONS

       -f     Fasta file containing all the [paired (-p 1) / unpaired (-p 0)] reads (required) paired reads must
              now be separated by ":"

       -s     Fasta  file  containing sequences to use as seeds exclusively (specify only if different from read
              set, optional)

       -m     Minimum number of overlapping bases with  the  seed/contig  during  overhang  consensus  build  up
              (default -m 16)

       -o     Minimum number of reads needed to call a base during an extension (default -o 3)

       -r     Minimum base ratio used to accept a overhang consensus base (default -r 0.7)

       -t     Trim  up  to  -t  base(s)  on  the  contig  end  when all possibilities have been exhausted for an
              extension (default -t 0)>

       -p     Paired-end reads used? (-p 1=yes, -p 0=no, default -p 0)

       -v     Runs in verbose mode (-v 1=yes, -v 0=no, default -v 0, optional)

       -b     Base name for your output files (optional)

       ============ Options below only considered with -p 1 ============

       -d     Mean distance expected/observed between paired-end reads (default -d 200, optional)

       -e     Error (%) allowed on mean distance   e.g. -e 0.75  == distance +/- 75% (default -e 0.75, optional)

       -k     Minimum number of links (read pairs) to compute scaffold (default -k 2, optional)

       -a     Maximum link  ratio  between  two  best  contig  pairs  *higher  values  lead  to  least  accurate
              scaffolding* (default -a 0.70, optional)

       -z     Minimum contig size to track paired-end reads (default -z 50, optional)

       -g     Fasta file containing unpaired sequence reads (optional)

SEE ALSO

       /usr/share/doc/ssake/SSAKE.readme between

AUTHORS

       This  manual  page was written by Andreas Tille <tille@debian.org> for the Debian system (but may be used
       by others).  Permission is granted to copy, distribute and/or modify this document under the terms of the
       GNU General Public License, Version 2 any later version published by the Free Software Foundation.

       On Debian systems, the complete text of the GNU General Public License can be found in /usr/share/common-
       licenses/GPL.

                                                  January 2008                                          SSAKE(1)