extract_fastq -- extracts sequence and quality from a trace or experiment file.
extract_fastq
[-
(abi
|alf
|scf
|ztr
|exp
|pln
)]
[-good_only
] [-clip_cosmid
] [-fasta_out
]
[-output
output_name] [input_name] ...
extract_fastq
extracts the sequence and quality information
from binary trace files or Experiment files. The input can be read
either from standard input or read from files listed directly as
arguments or contained within a "file of filenames". Output is
either sent to standard output or a named file. It contains the
sequence and confidence stored in single-line fastq format.
-abi
, -alf
, -scf
, -ztr
, -exp
, -pln
extract_seq
will automatically determine the correct input file
type. This option is supplied incase the automatic determination is
incorrect (which is possible, but has never been observed).
-output
file
-fofn
file_of_filenames
See section ExperimentFile(4).
See section scf(4).
@xref{Man-extract_seq extract_seq(1),Man-extract_seq extract_seq(1),extract_seq.1,,}.
Read
(4)