.TH srf2fastq 1 "December 10" "" "Staden io_lib"

.SH "NAME"

.PP
.BR srf2fastq
\- Converts SRF files to Sanger fastq format

.SH "SYNOPSIS"
.PP
\fBsrf2fastq\fR  [\fIoptions\fR] \fIsrf_archive\fR ...

.SH "DESCRIPTION"
.PP
\fBsrf2fastq\fR extracts sequences and qualities from one or more SRF
archives and writes them in Sanger fastq format to stdout.
.PP
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 \fIPhred\fR
style of quality encoding.

.SH "OPTIONS"
.PP
.TP
\fB-c\fR
Outputs calibrated confidence values using the ZTR \fBCNF1\fR
chunk type for a single quality per base. Without this use the
original Illumina \fI_prb.txt\fR files consisting of four quality
values per base, stored in the ZTR \fBCNF4\fR chunks.
.TP
\fB-C\fR
Masks out sequences tagged as bad quality.
.TP
\fB-s\fR \fIroot\fR
Generates files on disk with filenames starting \fIroot\fR, 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 \fB-S\fR parameter.
.TP
\fB-S\fR
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 \fB-s\fR parameter.
.TP
\fB-n\FR
When using -s the filename suffixes are simply numbered (starting with
1) instead of using the names listed in the SRF region chunks.
.TP
\fB-a\fR
Appends region index to the sequence names. Ie generate "name/1" and
"name/2" for a paired read.
.TP
\fB-e\fR
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.
.TP
\fB-r\fR \fIregion list\fR
Reverse complements the sequence and reverses the quality values for
all regions in the \fIregion list\fR. This is a comma separated list
of integer values enumerating the regions, starting from 1. Note that
this option only works when either \fB-s\fR or \fB-S\fR are
specified.

.SH "EXAMPLES"
.PP
To extract only the good quality sequences from all srf files in the
current directory using calibrated confidence values (if available).
.PP
.nf
    srf2fastq -c -C *.srf > runX.fastq
.fi
.PP
To extract a paired end run into two separate files with sequences
named \fIname\fR/1 and \fIname\fR/2.
.PP
.nf
    srf2fastq -s runX -a -n runX.srf
.fi
.PP
To extract a paired end run as a single file, alternating forward and
reverse sequences, with the second read being reverse complemented.
.PP
.nf
    srf2fastq -S -r 2 runX.srf > runX.fastq
.fi
.SH "AUTHOR"
.PP
James Bonfield, Steven Leonard - Wellcome Trust Sanger Institute