Assemblies post-processing tools

Various operations can be performed on cas assembly files.
Change the references and or read file names in a mapping file.
Extract a consensus sequence and get zero coverage regions.
Remove matches of low similarity.
Join a number of assemblies to the same reference.
Extract a part of an assembly
Extract unassembled reads from an assembly.
Extract reads from broken pairs.

If more advanced downstream analyses of assemblies are desired, the CLC Genomics Workbench can be used (see The Workbench uses the same de novo assembly and read mapping algorithms as the CLC Assembly Cell, so these tools can be directly run in the CLC Genomics Workbench, or alternatively, read mapping or assembly outputs created using CLC Assembly Cellcan be imported into the Workbench. However, note that the CLC Genomics Workbench requires a separate license to the CLC Assembly Cell.