train1

Overview

-h

(Help) This message

-nocall

Disable base recalling and just use the original called bases read from the input sample file

-recalln

Disable adding bases to or deleting from the original called sequence. Only recall Ns

-recallndb

Disable adding bases to or deleting from the original called sequence. Only recall Ns and dye blobs

-ladder

Similar to -recalln, but all bases, not only Ns will be recalled from original locations

-edited_bases

Start base recalling from the ABI's edited bases

-het

Call heterozygous bases

-mix

Call mixed bases

-min_ratio <ratio>

Override the default threshold ratio of heights of the lowest peak to the highest peak at a given position

-fr <repeat_fraction> Specify the repeat_fraction

(default is 0.85)

-fe <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)

-o <output_file>

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

-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)

-d <dir>

Read the input sample files from specified directory

-p <projectfile>

Specify the name of the projectfile which consists of two columns. Each line in this file contains the full path to the sample file to be processed and the full path to the FASTA file which contains the consensus sequence that should be used with this sample file