Consed

Consed is a graphical sequence editor and finishing tool designed to assist in the manual finishing of DNA sequence assemblies. It is part of the Phred/Phrap/Consed software ecosystem and is used to inspect, edit, and annotate shotgun sequencing projects. Consed provides an interactive environment for examining sequence reads, base calls, and quality scores, and for making editorial changes to improve assembly accuracy.

Key features include the visualization of chromatograms and assembly layout, tools to edit individual bases and trim low-quality regions, and support for resolving misassemblies and closing gaps. The program supports project-based workflows, enabling researchers to manage reads, track edits, and document finishing decisions. It also offers mechanisms to annotate reads, compare against reference sequences, and integrate finishing steps with downstream analyses. Output is compatible with common formats such as FASTA sequences and trace data, facilitating interoperability with other tools in the finishing pipeline.

History and context: Consed originated in the 1990s as part of the Phred/Phrap/Consed finishing platform developed to aid large-scale sequencing projects, including those associated with the Human Genome Project. It became a widely used graphical editor for manual finishing across a variety of organisms, especially in academic settings. Over time, its prominence declined with the emergence of newer assemblers and web-based finishing tools, but it remains cited for its role in enabling careful, user-driven refinement of complex assemblies.

Usage and availability: Consed is traditionally run on Unix-like systems with an X11 graphical interface; it has been distributed to academic users as part of the broader finishing toolkit. Documentation and community resources have supported users seeking to apply Consed to diverse sequencing projects.