4.1.B BASECALLING WITH LIFETRACE ON LINUX/UNIX SYSTEMS
About LifeTrace
The stand-alone basecaller,
LifeTrace, is written by Dirk Walters, Gábor Bartha and Macdonald Morris and
published in Genome Research, 11, 875-888, 2001. The performance of LifeTrace
with trace files produced by a MegaBace1000 sequencer fully confirms the benchmarks
reported in the paper.
How to get LifeTrace for Linux/Unix platforms
Unix/Linux versions of the LifeTrace can be downloaded from the LifeTrace
web site or be obtained by contacting me.
Post-process LifeTrace data with SEQtools
Provided chromatograms are basecalled on a Unix/Linux machine and the three
data files generated by LifeTrace
- - lifetrace.fasta
- - lifetrace.qscore.fasta
- - lifetrace.gap_qscore.fasta
subsequently transferred to a windows PC to make them available to SEQtools, the parameters for
- - assigning N's to low quality positions in the sequence
- - removing low quality regions at the start and end of the sequence
- - denoting atypical distances (gaps) between neighbor bases in the sequence
can be set by the user under Preferences/Chromatogram Import Settings in
SEQtools.
Below is shown a script (do1.com, kindly provided by Mogens Kjaer, Carlsberg Laboratory.)
which can be used to perform the basecalling on trace files located in the specified directory
on unix machines running different Linux/Unix operating systems:
- - lifetrace_linux
- - lifetrace_dec
- - lifetrace_sgi
- - lifetrace_sun
#!/bin/csh -f
foreach E ( *.abd )
set F=$E:r
lifetrace -c $E -out $F
echo $E done
end
The extension of the trace files (in this script = *.abd) must be changed to match the trace file extension. The script is run by
typing ./do1.com (or the name of the com file, in case you have saved the script under a different
name).
Before running the script, copy all chromatograms/trace files to be basecalled to a directory
on the Unix/Linux machine containing the do1.com script. Executing the script will basecall all trace files contained in the
directory to yield for each trace file:
- - the sequence in fasta format, *.fasta
- - a base quality data file, *.qscore.fasta
- - a gap quality data file, *.gap_qscore.fasta
The files must subsequently be moved back to the Windows PC for further processing by SEQtools.
See also the description of lifetrace command line options.