NAME
srf2fastq - Converts SRF files to Sanger fastq format
SYNOPSIS
srf2fastq [options] srf_archive ...
DESCRIPTION
srf2fastq extracts sequences and qualities from one or more SRF
archives and writes them in Sanger fastq format to stdout.
Note that Illumina also have a fastq format (used in the GERALD
directories) which differs slightly in the use of log-odds scores for
the quality values. The format described here is using the traditional
Phred style of quality encoding.
OPTIONS
-c Outputs calibrated confidence values using the ZTR CNF1 chunk
type for a single quality per base. Without this use the
original Illumina _prb.txt files consisting of four quality
values per base, stored in the ZTR CNF4 chunks.
-C Masks out sequences tagged as bad quality.
-s root
Generates files on disk with filenames starting root, one file
per non-explicit element in the SRF/ZTR region (REGN) chunk.
Typically this results in two files for paired end runs. The
filename suffixes come from the names listed in the SRF region
chunks. This option conflicts with the -S parameter.
-S Splits sequences into regions, but sequentially lists each
sequence region to stdout instead of splitting to separate files
on disk. This option conflicts with the -s parameter.
-n When using -s the filename suffixes are simply numbered
(starting with 1) instead of using the names listed in the SRF
region chunks.
-a Appends region index to the sequence names. Ie generate "name/1"
and "name/2" for a paired read.
-e Include any explicit sequence (ZTR region chunk of type ’E’) in
the sequence output. The explicit sequence is also included in
the quality line too. Currently this is utilised by ABI SOLiD to
store the last base of the primer.
-r region list
Reverse complements the sequence and reverses the quality values
for all regions in the region list. This is a comma separated
list of integer values enumerating the regions, starting from 1.
Note that this option only works when either -s or -S are
specified.
EXAMPLES
To extract only the good quality sequences from all srf files in the
current directory using calibrated confidence values (if available).
srf2fastq -c -C *.srf > runX.fastq
To extract a paired end run into two separate files with sequences
named name/1 and name/2.
srf2fastq -s runX -a -n runX.srf
To extract a paired end run as a single file, alternating forward and
reverse sequences, with the second read being reverse complemented.
srf2fastq -S -r 2 runX.srf > runX.fastq
AUTHOR
James Bonfield, Steven Leonard - Wellcome Trust Sanger Institute
December 10 srf2fastq(1)