Purpose

Attempts to estimate library complexity from sequence of read pairs alone. Does so by sorting all reads by the first N bases (5 by default) of each read and then comparing reads with the first N bases identical to each other for duplicates. Reads are considered to be duplicates if they match each other with no gaps and an overall mismatch rate less than or equal to MAX_DIFF_RATE (0.03 by default).

Reads of poor quality are filtered out so as to provide a more accurate estimate. The filtering removes reads with any no-calls in the first N bases or with a mean base quality lower than MIN_MEAN_QUALITY across either the first or second read.

Unpaired reads are ignored in this computation. The algorithm attempts to detect optical duplicates separately from PCR duplicates and excludes these in the calculation of library size.

Also, since there is no alignment to screen out technical reads one further filter is applied on the data. After examining all reads a Histogram is built of [#reads in duplicate set -> #of duplicate sets]; all bins that contain exactly one duplicate set are then removed from the Histogram as outliers before library size is estimated.

Dataset collections - processing large numbers of datasets at once

This will be added shortly

Inputs, outputs, and parameters

Either a SAM file or a BAM file must be supplied. Galaxy automatically coordinate-sorts all uploaded BAM files.

From Picard documentation( http://broadinstitute.github.io/picard/):

MIN_IDENTICAL_BASES=Integer   The minimum number of bases at the starts of reads that must be identical for reads to be
                              grouped together for duplicate detection.  In effect total_reads / 4^max_id_bases reads
                              will be compared at a time, so lower numbers will produce more accurate results but
                              consume exponentially more memory and CPU.  Default value: 5.

MAX_DIFF_RATE=Double          The maximum rate of differences between two reads to call them identical.  Default value:
                              0.03.

MIN_MEAN_QUALITY=Integer      The minimum mean quality of the bases in a read pair for the read to be analyzed. Reads
                              with lower average quality are filtered out and not considered in any calculations.
                              Default value: 20.

MAX_GROUP_RATIO=Integer       Do not process self-similar groups that are this many times over the mean expected group
                              size. I.e. if the input contains 10m read pairs and MIN_IDENTICAL_BASES is set to 5, then
                              the mean expected group size would be approximately 10 reads.  Default value: 500.

READ_NAME_REGEX=String        Regular expression that can be used to parse read names in the incoming SAM file. Read
                              names are parsed to extract three variables: tile/region, x coordinate and y coordinate.
                              These values are used to estimate the rate of optical duplication in order to give a more
                              accurate estimated library size. Set this option to null to disable optical duplicate
                              detection. The regular expression should contain three capture groups for the three
                              variables, in order. It must match the entire read name. Note that if the default regex
                              is specified, a regex match is not actually done, but instead the read name  is split on
                              colon character. For 5 element names, the 3rd, 4th and 5th elements are assumed to be
                              tile, x and y values. For 7 element names (CASAVA 1.8), the 5th, 6th, and 7th elements
                              are assumed to be tile, x and y values.  Default value:
                              [a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*.

OPTICAL_DUPLICATE_PIXEL_DISTANCE=Integer
                              The maximum offset between two duplicte clusters in order to consider them optical
                              duplicates. This should usually be set to some fairly small number (e.g. 5-10 pixels)
                              unless using later versions of the Illumina pipeline that multiply pixel values by 10, in
                              which case 50-100 is more normal.  Default value: 100.

Additional information

Additional information about Picard tools is available from Picard web site at http://broadinstitute.github.io/picard/ .