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) |