After you have performed a Sanger assembly and edited contigs —including removing sequences from them—you can elect to reassemble them. This reassembly respects any edits you have made to the contigs, but will update the alignment and gap positions.
To reassemble one or more contigs:
- From the Explorer panel table, select the contig(s) you want to reassemble.
- Choose one of the following commands.
- Contig > Reassemble contig ‘n’ individually (where ‘n’ is the contig number) or Reassemble selected contigs individually are the most commonly-used reassembly commands. These commands rearrange sequences within their original contigs and can be used to fix a possible misalignment or false join in specified contig(s). These commands reassemble sequences only within their original contig. When you use these commands, sequences are not moved outside their original contig and contigs are not allowed to merge.
- Contig > Reassemble contig ‘n’ within the project or Contig > Reassemble selected contigs within the project are less commonly used than the commands described above. These commands start by disassembling the reads within the selected contig(s). During the reassembly stage, the disassembled reads may be joined back together or may be incorporated into any of the other currently-selected contigs. These commands can be useful if you believe that sequences have been placed in the wrong contig, possibly due to an issue with repeats or with manual end-trimming. When you use these commands, contigs may merge, new contigs may be created, and/or sequences may be redistributed between the selected contigs. This is the type of reassembly done within SeqMan Ultra’s predecessor, SeqMan Pro.
- Contig > Reassemble contig ‘n’ individually (where ‘n’ is the contig number) or Reassemble selected contigs individually are the most commonly-used reassembly commands. These commands rearrange sequences within their original contigs and can be used to fix a possible misalignment or false join in specified contig(s). These commands reassemble sequences only within their original contig. When you use these commands, sequences are not moved outside their original contig and contigs are not allowed to merge.
*Notes:
* Reassembling a contig after using the Banana tool (
) in the Alignment view can result in unwanted mismatches.
* Reassembly acts only on the sequence data in the selected contig(s). It does not add any new data in the Unassembled view to the contig(s).
* If you want to perform the alignment using different parameters, we instead recommend starting a new SeqMan Ultra assembly from scratch.
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