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Table 1 Summary of NanoDJ notebooks

From: NanoDJ: a Dockerized Jupyter notebook for interactive Oxford Nanopore MinION sequence manipulation and genome assembly

Name

Functionality

0.0_QualityControl.ipynb

Evaluate the quality control and sequence handling

1.0_Basecalling.ipynb

Translates the events or the raw electrical signal from an ONT sequencer (FAST5 format) to a DNA sequence to obtain a FASTA or a FASTQ file

1.1_Trim+Demux.ipynb

Perform sequence trimming and demultiplexing

2.0_DeNovo_Canu-Miniasm.ipynb

De novo assembly with Canu or Miniasm, and polish with Racon and Pilon

3.0_DeNovo_Canu+polish.ipynb

Nanopolish modules to improve the Canu assembly

4.0_DeNovo_Flye.ipynb

De novo assembly with Flye software

5.0_DeNovo_Hybrid.ipynb

Perform de novo assembly of Nanopore reads in conjunction with Illumina reads using MaSuRCA and/or Unicycler software

6.0_AssemblyCompare.ipynb

Compare distinct assembly results based on QUAST software

7.0_SimulateReads.ipynb

Obtain simulated reads made with Nanosim software and the Nanosim-h fork with precomputed models

8.0_Alignment.ipynb

Reference-based assembly using either BWA, BLAST or Rebaler software

9.0_AssemblyGraph.ipynb

Assembly graph visualization

Educational.ipynb

Performs basecalling (with Albacore), quality control steps, and a BLAST-based classification of the reads (for educational purposes)