Parameters (defaults in brackets)

-L minimum percentage match 5' end (60)

sequencing vector searches and transposon search

-R minimum percentage match 3' end (80)

sequencing vector searches and transposon search

-m minimum 5' position

allows a minimum 5' end cutoff to be set if a sufficiently good match is not found (i.e. it is really a default 5' cutoff position). If a value of -1 is used the program will set the cutoff to be the distance between the primer and the cloning site.

-v vector-primer-pair filename

sequencing vector search using vector-primer-pair file

-V vector_primer length

the length of the sequence stored in the vector_primer file to use for the 5' search

-w word_length (4)

cloning vector search hash length

-P probability

cloning vector search, (a score less likely than P is a match)

-n num_diags (7)

cloning vector search, old score based algorithm: number of diagonals to combine

-d diagonal score (0.35)

cloning vector search, old score based algorithm

-l minimum match (20)

sequencing vector rearrangements and transposon search minimum match length

-M maximum vector length (100000)

all algorithms, reset for vectors >100000 bases

-p passed fofn

file of file names for passed files

-f failed fofn

file of file names for failed files

input fofn ...

input file of file names