RDNAssembler is a transcript based genome scaffolding and assembly tool written in perl. It requires perl 5.15 or greater, Moose, graph.pm, and bl2seq ( if used with -A option )
Input: psl file, genome assembly fasta file, transcript fasta file. Output: new DNA assembly.
Usage: --psl --rna --dna [options]
--A Try to assemble edges prior to scaffolding
--gap Takes same input as -scaffold option and will attempt to fill gaps and update alignment information prior to scaffolding
--dna DNA fasta file
--rna RNA fasta file
--psl Standard BLAT psl desribing alignments between sequences located in DNA and RNA fasta files
-h|--help prints this message
[options]:
[--pscore <Num> scaffolding path coverage score used to filter paths, ranges from 0 to 100 ( default 50 )]
[--nscore <Num> alignment coverage score used to filter alignments from psl, ranges from 0 to 100 ( default 1.6 )]
[--pid <Num> percentage of identity used to filter psl alignments ( default 98.1 )]
[--dcount <Int> maximum number of DNA sequences that each RNA sequence can be aligned to ( default 50 )]
[--match <Int> filter psl alignments with matched number of bases below this number (default 100)]
[--intron <Int> maximum intron size that can be represented by an edge ( default 100000 )]
[--overlap <Int> maximum base pairs that two DNA sequences can be overlapping on RNA before overlap is considered significant ( default 5 )]