Introduction

This repository contains code and data to analyze Amplicon sequencing runs of the NAO's phagemids. Samples were submitted for sequencing on 02 Feb 2023. More information on the sequencing run can be found in this NAO internal google doc.

Sequence Download

Sequences can be downloaded from this S3 bucket using the following command:

mkdir sequences
cd sequences
aws s3 cp s3://summer-seq-data/230203laura.tar .

You can then unzip, concatenate, and move them to the output directory

tar -xvf 230203laura.tar ;cd 230203laura ; gunzip *.fastq.gz

cat *.fastq > phagemid_amplicon_nanopore.fastq

mkdir ../../output/sequences ; mv phagemid_amplicon_nanopore.fastq ../../output/sequences/phagemid_amplicon_nanopore.fastq