DNA Dragon - DNA Sequence Contig Assembler Software

Features

Supported file formats

Loads sequence, trace or flowgram samples also by drag and drop:

• Project files
• XML DNA Dragon XML project (*.XML)
• Sequence file formats
• EMBL (*.eb;*.ebi;*.embl)
• GenBank (*.gb;*.gen;*.genbank;*.txt)
• FASTA (*.fa;*.fas;*.fast;*.fasta;*.fs;*.fsa;*.fsta)
• Next generation sequencing file formats
• ABI SOLiD files (*.gff)
• SOLiD CSFASTA files (*.csfasta)
• Solexa Compact ASCII Read Format, SCARF (s_*_sequence.txt)
• Illumina _seq.txt files (*.txt)
• Illumina FASTQ files (*.fastq)
• Illumina Qseq files (*_qseq.txt)
• 454 standard flowgram files (*.sff)
• Alignment file formats
• Sequence Alignment/Map (SAM) Format (*.sam)
• Binary Alignment Format (*.bam) (*.bam) [in progress]
• Trace file formats
• SCF (*.scf)
• ABI (*.abi;*.ab1)

Navigator tree

A sample navigator tree makes the project structure (contigs and samples) very clear. From here the samples are selected, then trimmed and assembled.

Trimming and untrimming features:

• Primer-Clipping
• Vector-Clipping with automatic pseudocircularization (50 bases). You can detect putative vector motifs in the sequences without any previous knowledge.
• Sequence quality-based trimming
• Length trimming
• Untimming: restores clipped ends.

Assembly machine and contig editor

Various options to change the assembly parameters are available. The fast, index-based assembly of sequences with automatic sorting of the sequences within the contigs (offset and trim ends) makes the project management a pleasure.
The proofreading of the contigs (sequence alignment), i.e. comparison of bases with their traces, and the export/copy of the consensus sequences is almost self-explanatory.