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 directo- ries) 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 Illu- mina _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 qual- ity 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 cur- rent 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 re- verse 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)
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