srf2fastq(1)							   Staden io_lib						      srf2fastq(1)

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. Typi-
	      cally 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)