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Command-line options

Input

Output

Extras

rPhrap Documentation Home

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Command-line Options
rPhrap Input
rPhrap Output
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Introduction
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Operation:

The rPhrap command-line tool can be operated in a manner very similar to the operation of Phrap. Differences are described more extensively in the linked pages below.

Expanded functionalilty:

• Read clusters can be built and assembled separately or in stages.
• Mate pair information is incorporated into the assembly process. Conflicting and confirming mate pairs are examined to determine whether two reads/contigs will be merged during assembly.
• Scaffolds (supertigs) are built based on mate pair information.
• An identity below which contigs/reads will not be merge can be specified.
• A merge algorithm based on percent identity is available, as an alternative to the tradition log likelihood ratio based algorithm.
• rPhrap can utilize multiple processors (available through Southwest Parallel Software).

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Running rPhrap
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Some other tips for running rPhrap:

• rPhrap does not need to be run from the same directory as the files that it reads in. So, a directory named rphrap_edit_dir (or any other name) can be created in the same directory as the Phrap edit_dir, so as not to overwrite the Phrap assembly output. Then rPhrap would be run from rphrap_edit_dir as:
  
    > rphrap ../edit_dir/foo.fasta
  
  The .qual and .cl files should be in the same directory as the .fasta file.

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Command-line Arguments
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Command-line arguments are significantly extended from Phrap.

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rPhrap Input
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rPhrap takes the same input files as does Phrap. Additionally, a mate-pair information file is required for the use of mate pairs in assembly or scaffold building, read cluster files can be pre-assembled and read into an assembly run, and a restart file can be created and read to for incremental assembly.

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rPhrap Output
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rPhrap creates the same output files as does Phrap, plus some additional ones. rPhrap output is described in the rPhrap output documentation.

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Extras
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Some scripts are provided for the visualization of rPhrap output.