converts SOLiD data to FASTQ data solid_to_fastq.py --input1=$input1 --input2=$input2 #if $paired.pairedSingle == "single": --input3="None" --input4="None" #else: --input3=$input3 --input4=$input4 #end if --output1=$output1 #if $paired.pairedSingle == "single": --output2="None" #else: --output2=$output2 #end if Single Paired paired['pairedSingle'] == 'paired'

**What it does** This tool takes reads and quality files and converts them to FASTQ data ( Sanger variant ). Any -1 qualities are converted to 1 before being converted to FASTQ. Note that it also converts sequences to base pairs. ----- **Example** - Converting the following sequences:: >1831_573_1004_F3 T00030133312212111300011021310132222 >1831_573_1567_F3 T03330322230322112131010221102122113 - and quality scores:: >1831_573_1004_F3 4 29 34 34 32 32 24 24 20 17 10 34 29 20 34 13 30 34 22 24 11 28 19 17 34 17 24 17 25 34 7 24 14 12 22 >1831_573_1567_F3 8 26 31 31 16 22 30 31 28 29 22 30 30 31 32 23 30 28 28 31 19 32 30 32 19 8 32 10 13 6 32 10 6 16 11 - will produce the following Sanger FASTQ data:: @1831_573_1004/1 AATACTTTCGGCGCCCTAAACCAGCTCACTGGGG + >CCAA9952+C>5C.?C79,=42C292:C(9/-7 @1831_573_1567/1 TTTATGGGTATGGCCGCTCACAGGCCAGCGGCCT + ;@@17?@=>7??@A8?==@4A?A4)A+.'A+'1,