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mira --project=ct --job=denovo,genome,accurate,454 -SK:not=8 &> log_assembly.txt & |
Getting .sff and Illumina .fastq files ready for Mira, and actually running Mira, can be automated using the a small script called "MiraWrapper.py". You provide MiraWrapper.py with your 454 and/or Illumina paired-end files, together with a project name and the Mira commands. If your 454 files are "454Reads.MID5.sff" and "454Reads.MID8.sff", and your paired-end Illumina files are "IlluminaReads1.fastq" and "IlluminaReads2.fastq", the syntax for running MiraWrapper is:
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MiraWrapper.py --project ct --sff 454Reads.MID5.sff 454Reads.MID8.sff --pe IlluminaReads1.fastq IlluminaReads2.fastq --mira --job=denovo,genome,accurate,454,solexa -SK:not=8 -notraceinfo &> log_assembly.txt &
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CAUTION: Note that the project name is specified by --project ct, and not in the usual mira parameters (like -project=ct. This is necessary so that MiraWrapper.py can keep track of all the intermediate file names. Also, MiraWrapper does not yet support information about mate-pair data, so you must run Mira with the -notraceinfo option.
If you have mate-pair data, you have to give mira information about the library sizes during sff_extract, for example:
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