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This repository is meant to accompany the paper "Ultra-rapid Sequencing-based Molecular Diagnostics via Real-Time Threshold Sequencing." It is a collection of scripts used to perform certain analysis from the paper, and shared for reproducibility.

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UltraRapidSeq

This repository is meant to accompany the paper "Ultra-rapid Sequencing-based Molecular Diagnostics via Real-Time Threshold Sequencing." It is a collection of scripts and data used to perform certain analysis from the paper, and shared for posterity and reproducibility.

VAF Over Time

Usage: python3 <guppy_generated_fastq> <bamfile> <VCF record>

Will sort fastq file based on Guppy timestamps and compute VAF support over time based on supplied VCF record.

PCR Cycle Sweep

Scripts to classify alignments into background reads, amplicon fragments, and on target reads.

Usage: find_amplicon_coverage_hist1h3b.sh <bamfile> Usage: find_amplicon_coverage_h3f3a.sh <bamfile>

bam_classifier.py

Re-implementation in pure python that should produce identical results to find_amplicon_coverage_xxx.sh. Usage: python3 bam_classifier.py <bamfile> <vcffile>

Calc Sampling Rate

Scripts to compute MinION Sampling Rate per channel, and the number of active/participating pores over time.

Usage: python3 calc_sampling_rate.py <guppy_generated_fastq> <analysis start time (s)> <analysis finish time (s)>

Common

basecall_fast5.sh

Simple guppy wrapper. Script was used to basecall SQK-RAD004 runs. These are the end-to-end experiments.

basecall_barcoded_fast5.sh

Simple guppy_wrapper. Script used to basecall SQK-RBK004 runs. These are the time-sweep/cycle-sweep experiments.

align_fastq.sh

Simple minimap2 wrapper.

sam_to_bam.sh

SAM to BAM conversion and secondary/supplementary alignment filtering.

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This repository is meant to accompany the paper "Ultra-rapid Sequencing-based Molecular Diagnostics via Real-Time Threshold Sequencing." It is a collection of scripts used to perform certain analysis from the paper, and shared for reproducibility.

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