tutorial.md

NanoBaseLib Tutorials

1. dataprep

combine_nanopolish_eventalign

python dataprep/combine_nanopolish_eventalign.py --input_file eventalign.txt

Input:

Parameter	Description
--input_file	Input eventalign filepath, the output from nanopolish eventalign.
--output_suffix	Output combined eventalign filename suffix
--n_processes	Number of processes to run.
--chunk_size	Number of lines from nanopolish eventalign.txt for processing.

Output:

File	Description
eventalign_combined.txt	The combined eventalign file.
eventalign.index	The index file for original eventalign file.

extract_tombo_resquiggle

python dataprep/extract_tombo_resquiggle.py

Input:

Parameter	Description
--root_dir	The root dir of tombo resquiggle resluts.
--folder	The folder of tombo resquiggle resluts. Default: "0".

Output:

File	Description
tombo_resquiggle.txt	Tombo resquiggle resluts.
tombo_summary.txt	The arrtibutes of tombo resquiggle resluts.

2. base_calling

generate_dna_dataset / generate_rna_dataset

Input:

Parameter	Description
--input_file	Input combined eventalign filepath.
--reference_file	Genome reference_file.
--fast5_folder	Orignal fast5 folder.
--save_folder	Save fast5 folder.

Output:

File	Description
Generated fast5 files.	Generated fast5 files saved in --save_folder, which correspond with the ground truth sequence.
label.csv	The the ground truth sequence file.

base_calling_dataloader

Input:

Parameter	Description
--fast5_folder	Input fast5 folder.
--label_file	Ground turth (label) file for each reads. Default: "label.csv".

Output:

File	Description
seg_data_arr.npy	Current signals.
seg_len_arr.npy	The length of current signals.
base_len_arr.npy	Ground turth sequence.
base_seq_arr.npy	The length of ground turth sequence.

base_calling_evaluation

Input:

Parameter	Description
--fast5_folder	Input fast5 folder.
--label_file	Ground turth (label) file for each reads. Default: "label.csv".

Output: The average accuracy of matches ($M$), mismatches ($X$), insertions ($I$), and deletions ($D$).

3. polya_detection

polya_detection_dataloader

4. segment_align

nanopolish_evaluation

tombo_evaluation

segpore_evaluation