train - interpretation of DNA Sanger sequencing data
- -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
This manpage was written by Andreas Tille for the Debian
distribution and can be used for any other usage of the program.