This is the command ssake that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
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)
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