srf2fastq - Man Page

srf2fastq  [options] srf_archive ...

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.

-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.

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

James Bonfield, Steven Leonard - Wellcome Trust Sanger Institute