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Command-line options

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Output

Extras

rPhrap Command Options Documentation 0

-CLF clone-library_filename
-C integer
-WR or -WRQ
-RR
-nmatch XX -nmatch NN
-IDENT float or integer
-MSLV integer
-NO_MATES
-ISMP
-M1
-NDC
-NS or -NO_STIGS
-TERSE
-CH string
-v96 or -V96

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Command-line argument:  -CLF clone-library_filename
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Clone Library File.

Directs rPhrap to use the specified file to ascertain clone lengths, rather than just "myfasta.cl". See the .cl file documentation for more information.

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Command-line argument:  -C integer
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Builds multi-sequence fasta files containing clusters of reads that share low-copy k-mers, i.e. reads that should assemble together. The integer specifies the number of cluster files that should be built. For how to use the read cluster files built in this manner, see the read cluster file documentation.