Home

Command-line options

Input

Output

Extras

rPhrap Input Documentation 1

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)

__________________________________
The .newcl file
__________________________________

(See the .newcl output documentation for information on how this file is generated.)

The ".newcl" file needs to be renamed to a ".cl" file in order to be automatically detected by rPhrap in the next assembly. By using this new file, you can iterate the assembly procedure, learning more about the mate pair length distributions on each assembly. Alternatively, you can specify the .newcl file using the command-line option -CLF.

__________________________________
Read cluster files (.rc)
__________________________________

rPhrap provides a mechanism for pre-assembling subcollections of reads inside of a larger set of reads. The user can collect the pre-assembly candidates into a single file and terminate the file name with a ".rc" appendix. This file naming convention signals to rPhrap that the designated file contains a read cluster, a collection of reads which should be independently pre-assembled before the main assembly algorithm. The ".rc" files can be placed in any order within the command-line list of input FASTA files, or they can be entries in a single ".fof", or file-of-files. As an example, a command line might look like:

    rphrap  -new_ace  foo1.fasta  foo2.fasta.rc  foo3.fasta  foo4.fasta.rc

This command would direct rPhrap to read in 4 multi-sequence fasta files, but to pre-assemble two of them separately before performing the main assembly.