NGS_analysis_pipeline

A pipeline written in python, for automatedly generating a series basic anaylses on cross-sectional or longitudinal NGS amplicon data

Dependecies:

1) pyhton3

2) scipy?

3) pandas

4) numpy

5) Biopython?

6) matplotlib

7) NGS_processing_pipeline (optional)?

...?

Required file naming format

PID_visitcode_weekspostinfection_generegion_primerversion_userID

Name		Name	Last commit message	Last commit date
Latest commit History 69 Commits
README.md		README.md
aa_threshold_finder.py		aa_threshold_finder.py
bubble_tree.py		bubble_tree.py
calc_average_normalized_pairwise_distance_for_alignment.py		calc_average_normalized_pairwise_distance_for_alignment.py
calc_dist_from_major_variant_cross_sectional.py		calc_dist_from_major_variant_cross_sectional.py
calc_divergence.py		calc_divergence.py
calc_divergence_cross_sectional.py		calc_divergence_cross_sectional.py
calc_entropy_aa_glycan_freq.py		calc_entropy_aa_glycan_freq.py
calc_entropy_aa_glycan_freq_cross_sectional.py		calc_entropy_aa_glycan_freq_cross_sectional.py
calc_haplotype_freq.py		calc_haplotype_freq.py
calc_multi_site_freq.py		calc_multi_site_freq.py
calc_v_loop_stats.py		calc_v_loop_stats.py
calc_variant_detection_limit.py		calc_variant_detection_limit.py
miseq_pacbio_tree.py		miseq_pacbio_tree.py
plot_aa_freq.py		plot_aa_freq.py
plot_aa_freq_cross_sectional.py		plot_aa_freq_cross_sectional.py
plot_divergence.py		plot_divergence.py
plot_divergence_cross_sectional.py		plot_divergence_cross_sectional.py
plot_entropy.py		plot_entropy.py
plot_glycan_freq.py		plot_glycan_freq.py
plot_loop_stats.py		plot_loop_stats.py
plot_mulit_site_freq.py		plot_mulit_site_freq.py
split_fasta_into_subfiles.py		split_fasta_into_subfiles.py
step_1_ngs_analysis_pipeline.py		step_1_ngs_analysis_pipeline.py
step_2_draw_tree.py		step_2_draw_tree.py