This is the command srf2fastq that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
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
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