ssake1

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)