convert from various base-FASTQ quality formats to fastqsangerFastQ_QualConverter.pl -i '$input_file' -f '$input_type' -o '$output_file'
**What it does**
This tool offers several conversions options relating to the FASTQ format.Output is always fastqsanger. Input can be specified or auto detected (based on first 15000 reads).
Hopefully it is faster than the default fastq groomer.
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**Quality Score Comparison**
::
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
...............................IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
..........................XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
!"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~
| | | | | |
33 59 64 73 104 126
S - Sanger Phred+33, 93 values (0, 93) (0 to 60 expected in raw reads) (sanger = input)
I - Illumina 1.3 Phred+64, 62 values (0, 62) (0 to 40 expected in raw reads) (sanger = input - 31)
X - Solexa Solexa+64, 67 values (-5, 62) (-5 to 40 expected in raw reads) (sanger = 33 + 10 * log(1 + 10 ** (input) - 64) / 10.0)) / log(10);
Diagram adapted from http://en.wikipedia.org/wiki/FASTQ_format
.. class:: infomark
Output from Illumina 1.8+ pipelines are Sanger encoded.