ComputeLibraryClusters

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For the assembly module, see ComputeLibStats.
ComputeLibraryClusters
Function Library analysis
Phase Post-processing
Standard CLAs PRE, DATA, RUN, GDB, NO_HEADER
Special CLAs LIBSTATS, INSERT_SIZES
Source location ARACHNE_DIR/reporting

ComputeLibraryClusters is a post-processing module that groups read libraries into clusters based on their average insert sizes. Its required input is the lib_stats subdirectory of RUN, which is generated by ComputeLibStats, and it outputs the text file library_clusters as well as the binary file reads.lib_clusters. These files constitute an optional but useful input to DisplaySupercontig.

Command-line arguments

Argument name Argument type Default value Meaning
LIBSTATS String lib_stats The input directory. The default name is the same as that of LIBSTATS_DIR in ComputeLibStats.
INSERT_SIZES Index list {0,2,4,10,40,200} Cluster centers (in kbp)

The clusters form around the center values by means of SnapToGrid. For example, given the default INSERT_SIZES, any library whose average insert size is in the interval (1,3] kbp will be put in the second cluster. A library whose average insert size is in (3,7] will be in the third cluster.

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