CLC Genomics Workbench allows for three types of output reporting:

• Assembly report: This will generate a summary report.
• List of non-assembled sequences: This will put all the reads that could not be assembled into a sequence list.
• Table including all contigs: de novo assembly can potentially generate a lot of contigs, and this option creates a table which makes it easier to get an overview of all the contigs. The table includes this information:
  1. Length of consensus sequence
  2. Number of reads
  3. Average coverage
  4. Total number of conflicts

Screenshot 1: The assembly report.

The information included in the report is:

• Reference sequences. For each contig this information is given:
  • The length of the contig
  • Number of matches (i.e. the number of reads that match the contig)
  • The minimum and maximum coverage in the contig.
• For read mapping, this information is given:
  • No coverage regions. A list of contigs and positions in contigs where there is no coverage.
  • Distribution of coverage. Distribution of coverage across all the contigs.
• Distribution of read length. For each sequence length, you can see the number of reads and the distribution in percent. This is mainly useful if you don't have too much variance in the lengths as you have in e.g. Sanger sequencing data.
• Distribution of matched reads lengths. Equivalent to the above, except that this includes only the reads that have been matched to a contig.
• Distribution of non-matched reads lengths. Show the distribution of lengths of the rest of the sequences.
• Summary statistics. A summary of the statistics above:
  • Reads. The number of reads and the average length.
  • Matches. The number of reads that match a contig and their average length.
  • Not matched. The number of reads that do not match a contig and their average length.
  • Coverage. The average coverage of all the contigs.