What it does
This tool converts Illumina QSEQ files into Phred FASTQ files.
Convert an Illumina QSEQ file into Phred FASTQ format in your Galaxy history for downstream tools that require fastq. Typically the output would be aligned with BWA or handled other Galaxy SRS tools.
The following data in QSEQ file format:
HWI-EAS431 1 3 100 1792 1317 0 1 ................................A...G..............A..GG....G............... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
Will be converted to FASTQ file format:
@3:100:1792:1317:N NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNANNNGNNNNNNNNNNNNNNANNGGNNNNGNNNNNNNNNNNNNNN +3:100:1792:1317:N
QSEQ format QSEQ files are the output of the Illumina pipeline. These files contain the sequence, corresponding qualities, as well as lane, tile and X/Y position of clusters.
According to Illumina manual qseq files have the following format:
FASTQ format A FASTQ file normally uses four lines per sequence. Line 1 begins with a '@' character and is followed by a sequence identifier and an optional description (like a FASTA title line). Line 2 is the raw sequence letters. Line 3 begins with a '+' character and is optionally followed by the same sequence identifier (and any description) again. Line 4 encodes the quality values for the sequence in Line 2, and must contain the same number of symbols as letters in the sequence.