INTRODUCTION.md

How to run your sample 101

Step 1

A simple bioconda installation:

conda install minorseq

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Step 2

Create CCS2 reads from your sequel chip

Juliet currently uses PacBio CCS reads as input. The use of CCS rich QVs allows sensitive minor variant calling.

ccs m54000_170101_050702_3545456.subreadset.xml yourdata.ccs.bam

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Step 3

Filter CCS reads as described here: JULIETFLOW.md#filtering

To ensure a uniform noise profile, we filter to 99% predicted accuracy. Barcode demultiplexing might be done.

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Step 4

Download the reference sequence of interest as ref.fasta

Juliet currently calls amino acid variants to a given refrence sequence so they might be easily related to known variants.

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Step 5

Create a target-config for your gene as described here: JULIET.md#target-configuration

The target-config specifies Open Reading and how specific amino acids should be labeled in output results (ie Disease Resistant Mutation variants)

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Step 6

Run julietflow

The calling sequence is very simple taking sequencing reads, the reference, and the reference annotation config.

julietflow -i yourdata.filtered.ccs.bam -r ref.fasta -c targetconfig.json

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Step 7

Interpret results in yourdata.json or yourdata.html

'yourdata.html' is easily viewed in a web browser and reflects the underlying results stored in 'yourdata.json'