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Assembles microbial genomes, like other tools, but with the differences that it handles different types of short and long reads so that it can make hybrid assemblies.

The documentation leaves some unanswered questiosn in terms of how to run the program. There are however some basic examples:

unicycler -1 short_reads_1.fastq.gz -2 short_reads_2.fastq.gz -l long_reads.fastq.gz -o output_dir

The question is, whether two sets of short reads can be combined in a single command line.

To make note of

  • Unicycler uses python3