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)