trainphd1

Overview

-h

(Help) This message

-C <consensusfile>

Specify the name of the FASTA file which contains the consensus sequence

-V <vector>

Specify the name of the FASTA file which contains the vector sequence

-P <primer>

Specify the name of the FASTA file which contains the primer sequence

-S <site>

Specify the name of the FASTA file which contains the restriction site sequence

-M <match>

Specify the match premium (default is 10)

-X <mismatch>

Specify the mismatch penalty (default is 20)

-G <gap_penalty >

Specify the gap initiation or extension penalty (default is 40)

-r <repeat_fraction>

Specify the repeat_fraction (default is 0.85)

-f <max_frac_of_err>

Specify the allowable fraction of errors within the best alignment region. Default is 0.1. If actual fraction of errors exceeds this vale, the fragment will be rejected (=not used in training process)

-a <min_portion_aligned> Instructs trainphd to ignore a read if less than

the specified portion of its bases is aligned with reference sequence (default is 0)

-l <min_read_length>

Instructs trainphd to ignore a read of length less than specified number of basepairs (0 by default)

-o <output_file>

Specify the name of the output file. By default, the output will be made to stdout

-t <tab_dir>

Instructs trainphd extract alternative base calls from TAB files stored in directory tab_dir and to output these calls, together with quality value for each alternative call

-d <dir>

Read the input PHD files from specified directory

-j <projectfile>

Specify the name of the projectfile which comprises two columns: the full path to the FASTA file which contains the consensus sequence, followed by the full path to the sample file