Qual

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Qual is a standard file format for read and contig quality scores. The corresponding format for base identities is fasta. It is produced by most base-calling software, such as PHRED. Qual and its binary companion format, qualb, are the quality score formats recognized by Arachne.

Here is an example of a qual-format read:

> L1000ABCDEFG.readname
5 8 10 10 9 10 11 19 9 9 10 12 14 21 12
14 21 21 34 34 34 33 33 33 28 24 16 14 19 11
15 23 18 31 33 24 24 30 30 30 49 49 49 49 49 
49 49 49 49 45 45 37 37 37 37 50 50 50 50 50
50 38 38 23 39 ...

Each integer is a Q-value (see Quality score) and corresponds to one of the bases in the read. Each qual-format read should have a name equal to that of a fasta- or fastb-format read in the Arachne input. The number of integers should be equal to the number of bases on the corresponding fasta read; if it is not, Arachne will throw out the read.

Directory

qual is also the name of an input directory. It is a subdirectory of DATA and contains the raw data for all read quality scores, in qual format.

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