Identification of Polymorphic Markers for Genetic Mapping - Genomics: Essential Methods - page 39

Table 2.2 Common command-line options for the Phred program.

Parameter Argument Default Description

-help None None Display helpful information

-if < filename > None Read input filenames from file

-id

< dirname >

None Read input files from < dirname >

-s None Nofile Write × .seq sequence file(s)

-sa < filename > None Append sequence files to

< filename >

-sd < dirname > Nofile Write × .seq file(s) to < dirname >

-q None Nofile Write × .qual quality file(s)

-qa < filename > None Append quality files to < filename >

-qd < dirname > Nofile Write × .qual file(s) to < dirname >

-c None Nofile Write × phred SCF file(s)

-cd < dirname > Nofile Write × SCF file(s) to < dirname >

-d None Nofile Write × .poly poly file(s)

-dd < dirname > Nofile Write × .poly file(s) to < dirname >

-trim_alt < enzyme seq > Notrim Enable alternate auto trim

-trim_cutoff < n > 0.05 Trim_alt error probability

-trim_fasta None None Trim FASTA bases and qual. values

-trim_scf None None Trim SCF bases and qual. values

-trim_phd None None Trim base call data in phd files

-process_nomatch None None Process chromats with unmatchable

primerID string

Notes
o Available from http://www.phrap.org/phredphrap/phred.html [17]. For common command-line
options, see Table 2.2.
p For a complete listing of command-line options, invoke Phred with the -help option.

2.2.2.6 Sequence alignment and assembly

To perform variant discovery with resequencing data, it is necessary to anchor sequence
reads on a reference sequence for making comparisons (alignment), and it is usually advis-
able to layer multiple overlapping reads on the reference to generate a consensus call at
each base (assembly). The cross_match and Phrap [18] programs created by the University
of Washington are commonly used to perform such tasks with capillary-based resequencing
data. The reference sequence input to Phrap must be in trace file (SCF) format and can