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)