fastx_toolkit
zcat -f $input | fastx_quality_stats -o $output -Q 33
**What it does**
Creates quality statistics report for the given Solexa/FASTQ library.
.. class:: infomark
**TIP:** This statistics report can be used as input for **Quality Score** and **Nucleotides Distribution** tools.
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**The output file will contain the following fields:**
* column = column number (1 to 36 for a 36-cycles read Solexa file)
* count = number of bases found in this column.
* min = Lowest quality score value found in this column.
* max = Highest quality score value found in this column.
* sum = Sum of quality score values for this column.
* mean = Mean quality score value for this column.
* Q1 = 1st quartile quality score.
* med = Median quality score.
* Q3 = 3rd quartile quality score.
* IQR = Inter-Quartile range (Q3-Q1).
* lW = 'Left-Whisker' value (for boxplotting).
* rW = 'Right-Whisker' value (for boxplotting).
* A_Count = Count of 'A' nucleotides found in this column.
* C_Count = Count of 'C' nucleotides found in this column.
* G_Count = Count of 'G' nucleotides found in this column.
* T_Count = Count of 'T' nucleotides found in this column.
* N_Count = Count of 'N' nucleotides found in this column.
For example::
1 6362991 -4 40 250734117 39.41 40 40 40 0 40 40 1396976 1329101 678730 2958184 0
2 6362991 -5 40 250531036 39.37 40 40 40 0 40 40 1786786 1055766 1738025 1782414 0
3 6362991 -5 40 248722469 39.09 40 40 40 0 40 40 2296384 984875 1443989 1637743 0
4 6362991 -4 40 248214827 39.01 40 40 40 0 40 40 2536861 1167423 1248968 1409739 0
36 6362991 -5 40 117158566 18.41 7 15 30 23 -5 40 4074444 1402980 63287 822035 245
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This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
.. __: http://hannonlab.cshl.edu/fastx_toolkit/