AAARF v 1.0.1
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- To use AAARF you will need a fasta file of genomic sample sequences, preferably sorted in order of sample repetitiveness. he .group file from either clusterReport and/or queryOrthoMCL and the Map file from the Cluster Orthologs and Paralogs and Assemble Custom Gene Sets workflow.
Example Data
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Community Data -> iplantcollaborative -> example_data -> aaarf -> input -> ZU_1000.fasta
Parameters Used in App
BLAST AND MCS CONSTRUCTION PARAMETERS (shown with default values)
maxBlastHits = 100 maximum number of hits used to construct coverage matrix
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BL2SEQ_e = 1e-10; maximum evalue for BL2SEQ hit
EXTENSION PARAMETERS (shown with default values)
maxExtendHits = 1000; maximum number of BLAST hits used to extend build
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minOverlapLen = 90; minimum required overlap between MCS and New Query Sequence for BL2SEQ, based on 50% of minCoverLen times_used = 13; Maximum number of times that a sequence is used in each direction
Output File(s)
inputFile_AAARF.fasta - main output file with assemblies of high-copy number repeats
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AAARF_log - detailed log of all AAARF activities formatted based on log4Perl perl module
Output File(s)
inputFile_AAARF.fasta - main output file with assemblies of high-copy number repeats
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