DNPTrapper

DNPTrapper combines relatively simple but powerful algorithms with visualization of problematic assembly locations, thus providing detailed information for biologists and allowing rapid decision making to make necessary corrections. The main goal of DNPTrapper is to provide more power to the user than other finishing tools. The user can move sequences using drag and drop; re-align them; cut, copy, and paste them; run algorithms on them; add and remove features; choose between view modes; zoom in and out. The user interface is a front end to a database, and changes made using Trapper are automatically propagated to the database. DNPTrapper is essentially an editor that visualizes assemblies of shotgun sequence fragment reads as gapped multiple alignments. The assemblies can be produced by any assembler that produces the supported file formats (e.g. .ace-files from Phrap), and can be exported to the same format after repeat analysis and resolution. In addition to the read sequences, different features and data such as DNPs, vector sequence, quality values, chromatograms and mate pairs are visualized in the editor according to the preferences of the user. Sequence features can be present in the input assembly files, or be added during the finishing process by running default built-in algorithms that detect and label the desired features. DNPTrapper runs under Linux and requires Qt 3 and the Berkeley DB. DNPTrapper was developed using Berkeley DB version 4.3 and should work with later versions.