Consed:A Finishing Package (BAM File Viewer, Assembly Editor, Autofinish, Autoreport, Autoedit, and Align Reads To Reference Sequence)

Why Use Consed?

1. Supports Illumina, 454, other Next-Gen and Sanger Reads and allows mixtures of these read types
2. Consed now includes BamScape which can view bam files with unlimited numbers of reads. BamScape can bring up consed to edit reads and the reference sequence in targetted regions.
3. Consed is compatible with Newbler, Cross_match, Phrap, MIRA, Velvet and PCAP output.
4. Quickly takes the user to each variant site for viewing (also available as an automated report)
5. Overview of assembly can help detect and fix misassemblies
6. Consed is licensed to over 4000 sites and climbing. In *active* use at over 230 sites in 36 countries including biotech, chemical, pharmaceutical, and agricultural companies, major genome centers, small academic labs, and government labs
7. Editing time reduced by the program's ability to pin-point problem areas
8. Editing is guided by error probabilities
9. Consed is able to pick primers very successfully (98 out of 98 in a controlled study). Labs that use it are quite happy with it.
10. Able to pick PCR primers to amplify a region, even if you only have a fasta file for the region

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