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Fig. 2 | BMC Genomics

Fig. 2

From: The effect of variant interference on de novo assembly for viral deep sequencing

Fig. 2

Workflow diagram of the investigation of variant simulated NGS reads through de novo assembly. First, in step 1, an artificial reference genome and corresponding initial variant reads were created with varying constraints such as genome length, GC content, read length, and assemblers, according to the experiment types as detailed in Supplement Figure S1. In the second step, an artificial mutated variant genome was created. The process is repeated to generate 247 different mutated variants with controlled mutation parameters— starting with 1 mutation every 4 nucleotides (75% PID) and ending with 1 mutation in every 250 nucleotides (99.6% PID). Mutated variant reads are also generated for each of the mutation parameters. In the third and fourth steps, the initial and mutated variants were then combined and used as input for de novo assembly for the three experiments, as detailed in Supplement Figure S1

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