Nanopore测序序列组装以及菌种鉴定

GenomeAssembly.png

Officially recommendflye to conduct sequence assembly in Nanopore website.

conda install -y flye

flye --nano-raw ~/project/ONT/basecalling_gpu_sup/pass/BL21.fastq.gz -g 4.6m -o ~/project/ONT/basecalling_gpu_sup/6_flye -t 15 -i 3

Output

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View the assembled genome sequences

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Using flye to conducted genome assembly, we get two cycle sequences, one is about 5M in size (genome), and the other is about 11k in size (plasmid).

Taxonomy Analysis

After assembling, we start to classify them directly by using theKraken2 tools which is commonly used.

• Taxonomy Analysis result

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The output of kraken-report is tab-delimited, with one line per taxon. The fields of the output, from left-to-right, are as follows:

1. Percentage of reads covered by the clade rooted at this taxon

2. Number of reads covered by the clade rooted at this taxon

3. Number of reads assigned directly to this taxon

4. A rank code, indicating Unclassified, Domain, Kingdom, Phylum, Class, Order, Family, Genus, or Species..

5. NCBI Taxonomy ID

6. The indented scientific name