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rPhrap Output Documentation 0

Introduction
The .newcl file
Paired-end info file
Memory Usage
Merge Conflict Table
Assembly Stats by Contig
Singleton Mate Pairs
Mate Pair Stats
Mate Pair Conflicts
Mate Pair Conflict Stats
Supertigs
Supertig Summary
Supertig/Contig Use Matrix
Subclone Length Histograms
Usage Statistics

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Introduction
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Sections of the rPhrap output (which, as in Phrap, goes to STDOUT by default and can be redirected to a file) are discussed here in the order in which they first appear in the output.

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Output File Section: The .newcl file
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On each rPhrap run, a new output file appended with ".newcl" is generated. In this file appears each of the subclone families along with length information computed during the assembly. If enough pairs of a subclone family are assembled, rPhrap computes a least-squares fit to a gaussian for the family distribution and prints out an entry in the .newcl file specifying a minimum, average, and maximum length for the family, based on a 3 sigma cutoff point above and below the average family length. The computed standard deviation is also appended to the entry as a comment. If there is not enough information to determine a least-squares fit, then the entry will have just the family name and a comment with the number of pairs assembled by rPhrap.

Here are some of the rules followed regarding the .cl file:

• If there is no .cl file:
  • rPhrap runs with no mate pair constraints and builds a .newcl file based on assembly with no constraints. rPhrap guesses at the family names.
• If there is a .cl file
  • If a line in the .cl file specifies a family name, rPhrap calculates the resulting size of this family and uses this to build the .newcl file.
  • If a line in the .cl file specifies both a family name and clone sizes, rPhrap uses all of this information to assemble and builds a .newcl based on the resulting assembly.