converts between FASTQ data and other data formats
fastq_conversions.py
--command=$conversionType.type
--input=$input
#if $conversionType.type == "sol2std":
--outputFastqsanger=$outputFastqsanger
#else:
--outputFastqsanger="None"
#end if
#if $conversionType.type == "std2sol":
--outputFastqsolexa=$outputFastqsolexa
#else:
--outputFastqsolexa="None"
#end if
#if $conversionType.type == "fq2fa":
--outputFasta=$outputFasta
#else:
--outputFasta="None"
#end if
conversionType['type'] == 'sol2std'conversionType['type'] == 'std2sol'conversionType['type'] == 'fq2fa'
**What it does**
This tool offers several conversions options relating to the FASTQ format.
-----
**Examples**
- Converting the Solexa/Illumina FASTQ data::
@081017-and-081020:1:1:1715:1759
GGACTCAGATAGTAATCCACGCTCCTTTAAAATATC
+
II#IIIIIII$5+.(9IIIIIII$%*$G$A31I&&B
- will produce the following Sanger FASTQ data::
@081017-and-081020:1:1:1715:1759
GGACTCAGATAGTAATCCACGCTCCTTTAAAATATC
+
++!+++++++!!!!!"+++++++!!!!)!%!!+!!%!
- Converting standard Sanger FASTQ::
@1831_573_1004/1
AATACTTTCGGCGCCCTAAACCAGCTCACTGGGG
+
><C&&9952+C>5<.?<79,=42<292:<(9/-7
@1831_573_1050/1
TTTATGGGTATGGCCGCTCACAGGCCAGCGGCCT
+
;@@17?@=>7??@A8?==@4A?A4)&+.'&+'1,
- will produce the following Solexa/Illumina FASTQ data::
@1831_573_1004/1
AATACTTTCGGCGCCCTAAACCAGCTCACTGGGG
+
][bEEXXTQJb]T[M^[VXK\SQ[QXQY[GXNLV
@1831_573_1050/1
TTTATGGGTATGGCCGCTCACAGGCCAGCGGCCT
+
Z__PV^_\]V^^_`W^\\_S`^`SHEJMFEJFPK
- Converting the Sanger FASTQ data::
@1831_573_1004/1
AATACTTTCGGCGCCCTAAACCAGCTCACTGGGG
+
><C&&9952+C>5<.?<79,=42<292:<(9/-7
@1831_573_1050/1
TTTATGGGTATGGCCGCTCACAGGCCAGCGGCCT
+
;@@17?@=>7??@A8?==@4A?A4)&+.'&+'1,
- will produce the following FASTA data::
>1831_573_1004/1
AATACTTTCGGCGCCCTAAACCAGCTCACTGGGG
>1831_573_1050/1
TTTATGGGTATGGCCGCTCACAGGCCAGCGGCCT