Download CLC Genomics Workbench

CHAPTER 2. HIGH-THROUGHPUT SEQUENCING
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Trim summary.
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Name. The name of the sequence list used as input.
Number of reads. Number of reads in the input file.
Avg. length. Average length of the reads in the input file.
Number of reads after trim. The number of reads retained after trimming.
Percentage trimmed. The percentage of the input reads that are retained.
Avg. length after trim. The average length of the retained sequences.
Read length before / after trimming. This is a graph showing the number of reads of
various lengths. The numbers before and after are overlayed so that you can easily
see how the trimming has affected the read lengths (right-click the graph to open it in
a new view).
Trim settings A summary of the settings used for trimming.
Detailed trim results. A table with one row for each type of trimming:
∗ Input reads. The number of reads used as input. Since the trimming is done
sequentially, the number of retained reads from the first type of trim is also the
number of input reads for the next type of trimming.
∗ No trim. The number of reads that have been retained, unaffected by the trimming.
∗ Trimmed. The number of reads that have been partly trimmed. This number plus
the number from No trim is the total number of retained reads.
∗ Nothing left or discarded. The number of reads that have been discarded either
because the full read was trimmed off or because they did not pass the length
trim (e.g. too short) or adapter trim (e.g. if Discard when not found was chosen
for the adapter trimming).
Click Next if you wish to adjust how to handle the results (see section ??). If not, click Finish.
This will start the trimming process.
If you trim paired data, the result will be a bit special. In the case where one part of a paired read
has been trimmed off completely, you no longer have a valid paired read in your sequence list.
In order to use paired information when doing assembly and mapping, the Workbench therefore
creates two separate sequence lists: one for the pairs that are intact, and one for the single
reads where one part of the pair has been deleted. When running assembly and mapping, simply
select both of these sequence lists as input, and the Workbench will automatically recognize that
one has paired reads and the other has single reads.
2.4
De novo assembly
The de novo assembly algorithm of CLC Genomics Workbench offers comprehensive support for
a variety of data formats, including both short and long reads, and mixing of paired reads (both
insert size and orientation).
The de novo assembly process has two stages:
1. First, simple contig sequences are created by using all the information that are in the read
sequences. This is the actual de novo part of the process. These simple contig sequences
do not contain any information about which reads the contigs are built from. This part is
elaborated in section 2.4.1.