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)