1srf2fastq(1)                     Staden io_lib                    srf2fastq(1)
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NAME

6       srf2fastq - Converts SRF files to Sanger fastq format
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SYNOPSIS

10       srf2fastq  [options] srf_archive ...
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DESCRIPTION

14       srf2fastq  extracts  sequences  and  qualities from one or more SRF ar‐
15       chives and writes them in Sanger fastq format to stdout.
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17       Note that Illumina also have a fastq format (used in the GERALD  direc‐
18       tories)  which  differs  slightly in the use of log-odds scores for the
19       quality values. The format described  here  is  using  the  traditional
20       Phred style of quality encoding.
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OPTIONS

24       -c     Outputs  calibrated  confidence  values using the ZTR CNF1 chunk
25              type for a single quality per base. Without this use the  origi‐
26              nal  Illumina  _prb.txt  files consisting of four quality values
27              per base, stored in the ZTR CNF4 chunks.
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29       -C     Masks out sequences tagged as bad quality.
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31       -s root
32              Generates files on disk with filenames starting root,  one  file
33              per  non-explicit  element  in  the SRF/ZTR region (REGN) chunk.
34              Typically this results in two files for  paired  end  runs.  The
35              filename  suffixes  come from the names listed in the SRF region
36              chunks.  This option conflicts with the -S parameter.
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38       -S     Splits sequences  into  regions,  but  sequentially  lists  each
39              sequence region to stdout instead of splitting to separate files
40              on disk. This option conflicts with the -s parameter.
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42       -n     When using -s the filename suffixes are simply numbered  (start‐
43              ing  with 1) instead of using the names listed in the SRF region
44              chunks.
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46       -a     Appends region index to the sequence names. Ie generate "name/1"
47              and "name/2" for a paired read.
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49       -e     Include  any explicit sequence (ZTR region chunk of type 'E') in
50              the sequence output. The explicit sequence is also  included  in
51              the quality line too. Currently this is utilised by ABI SOLiD to
52              store the last base of the primer.
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54       -r region list
55              Reverse complements the sequence and reverses the quality values
56              for  all  regions  in the region list. This is a comma separated
57              list of integer values enumerating the regions, starting from 1.
58              Note that this option only works when either -s or -S are speci‐
59              fied.
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EXAMPLES

63       To extract only the good quality sequences from all srf  files  in  the
64       current directory using calibrated confidence values (if available).
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66           srf2fastq -c -C *.srf > runX.fastq
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68       To  extract  a  paired  end  run into two separate files with sequences
69       named name/1 and name/2.
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71           srf2fastq -s runX -a -n runX.srf
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73       To extract a paired end run as a single file, alternating  forward  and
74       reverse sequences, with the second read being reverse complemented.
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76           srf2fastq -S -r 2 runX.srf > runX.fastq
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AUTHOR

79       James Bonfield, Steven Leonard - Wellcome Trust Sanger Institute
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83                                  December 10                     srf2fastq(1)