The Contig table

The Contig Table is almost identical to the table generated by the de novo assembly tool with the difference that two extra columns have been added: Contig matches length describes the length of contig matches. This value is the sum of all the aligned contig bases of all the hits on the reference. "Contig matches count" describes the number of matches found for each contig.

The Contig table allows the following functions:

Show Contigs. Shows the contigs. If the contigs used as input had reads mapped to them this action displays the read mapping.
Add/Extract. Makes it possible to add additional contigs or to extract contigs to be handled with other tools (described in section 3.2.5).
Copy Contig. Makes one or more copies of the selected contig. Reads mapped to the original contig are extracted and mapped again with the original contig and all copies as a reference. The result of this mapping is an even distribution of the reads across all copies of the contig.
Map Reads. Allows the read mapping of contigs to be updated in two different ways. The "Map Reads Again" function extracts reads from the selected contigs and re-map each read to its source contig. The "Replace all reads" function allows the user to select one or more data sets containing reads, which are then used to replace all reads mapped to all contigs.
Join Contigs. Function for joining contigs in two different ways. The automatic join uses BLAST to find overlaps between two contigs and the manual gap method can be used to join sequential and non-overlapping contigs when the orientation and gap distance is known. The "Join Contigs" function is described in Joining contigs.
Remove Contigs. Makes it possible to remove contigs e.g. when no mapping is seen to the reference or if very low coverage is observed.