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. 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.
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