Category
Format Conversion
Usage
lavToAxt in.lav tNibDir qNibDir out.axt
Manual
This tool is part of UCSC Genome Browser's utilities.
tNibDir/qNibDir are either directories full of nib files, or a single twoBit file
Options
- -fa qNibDir: is interpreted as a fasta file of multiple dna seq instead of directory of nibs
- -tfa tNibDir: is interpreted as a fasta file of multiple dna seq instead of directory of nibs
- -dropSelf: drops alignment blocks on the diagonal for self alignments
- -scoreScheme=fileName: Read the scoring matrix from a blastz-format file. (only used in conjunction with -dropSelf, to rescore alignments when blocks are dropped)
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