rPhrap Input Documentation 3

rPhrap version 4.23 and higher

Mate pair library (.cl) files
Mate pair library names
The .newcl file
Read cluster files (.rc)
Multi-file sequence input
Excluded reads (.excl) files
Restart files (incremental assembly)

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Restart files (incremental assembly)
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If a restart file has been created, rPhrap detects the existence of "new" sequences (sequences that have not already been processed) and will automatically perform an "incremental assembly" to save time.

The new sequences must be both:
    a) in a new file or set of new files
  and
    b) at the end of the list of files

For example, in the case that you generated an assembly via the rPhrap command line:

rphrap -WR fooseqs1 > fooseqs1.out

or the case that you generated a pre-assembly via the command line:

rphrap -WRQ fooseqs1 > fooseqs1.out

... then you can add sequences to the assembly via the command line:

rphrap -RR fooseqs1 newseqs > fooseqs1.out

rPhrap will add the new sequences to the pre-assembly and then generate a new assembly.

( For more information, see the -WR/-WRQ documentation. )

( Note that sequences are compared and scored in a different order when using incremental assembly versus a non-restarted assembly. Therefore, the assembly probably will be slightly different because of the effects of sorting scores of equal value. There is no guarantee that the differnet assembly is better or worse. Phrap has always exhibited this behavior. Scrambling of input sequences almost always will produce slightly different assemblies. )

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