rpetit3

# ===========================================================================
#
#                            PUBLIC DOMAIN NOTICE
#               National Center for Biotechnology Information
#
#  This software/database is a "United States Government Work" under the
#  terms of the United States Copyright Act.  It was written as part of
#  the author's official duties as a United States Government employee and
#  thus cannot be copyrighted.  This software/database is freely available
#  to the public for use. The National Library of Medicine and the U.S.

rpetit3

library("ggplot2")
files <-dir("/home/rpetit/projects/narsa/remaps/coverages_agr", pattern =".txt")
for(iin1:length(files)) {
    name <-gsub("-cov.txt$", "", files[i])
    # Read Coverage File
    file_path =paste0("/home/rpetit/projects/narsa/remaps/coverages_agr/", files[i])
    coverage <-read.table(file_path, sep="\t", header=FALSE)
    colnames(coverage) <-c("reference", "position", "coverage")
    max_x =nrow(coverage)
    max_y =max(coverage$coverage) + 10

rpetit3

sudo apt-get update && sudo apt-get install -y \
    build-essential \
    libssl-dev \
    uuid-dev \
    libgpgme11-dev \
    squashfs-tools \
    libseccomp-dev \
    pkg-config \
    git \
    cryptsetup-bin \

rpetit3

#!/usr/bin/env nextflow

// Input parameters
params.genbank = "./NRS384.gbk"
params.fastq = "fastq_files"
params.pattern = "N*P{1,2}_trim.fq.gz"
params.outdir = "breseq_analysis_results"

// Reference and paired read channels
fastq_file_path = "$params.fastq/${params.pattern}"

rpetit3

# The Base AMI should be an ECS-optimized Amazon Linux 2 AMI
# Create the AMI with ~30-50GB of storage to allow for programs and temporary storage.

sudo yum install -y bzip2 wget git emacs

# Install AWS CLI to ${HOME}
wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
bash Miniconda3-latest-Linux-x86_64.sh -b -f 
~/miniconda3/bin/conda init bash
source ~/.bashrc

rpetit3

#! /usr/bin/env nextflow
import groovy.json.JsonSlurper
import groovy.text.SimpleTemplateEngine
import groovy.util.FileNameByRegexFinder
import java.nio.file.Path
import java.nio.file.Paths
import nextflow.util.SysHelper
PROGRAM_NAME = workflow.manifest.name
VERSION = workflow.manifest.version

rpetit3

Started here: https://nextstrain.org/docs/getting-started/introduction

Installation

Installed on Chlamy (behind Emory VPN)

mkdir nextstrain
cd nextstrain
curl http://data.nextstrain.org/nextstrain.yml --compressed -o nextstrain.yml
conda env create -f nextstrain.yml
conda activate nextstrain

rpetit3

>X17403.1:c80631-76903 Human cytomegalovirus strain AD169 complete genome
ATGTTTTTCAACCCGTATCTGAGCGGCGGCGTGACCGGCGGTGCGGTCGCGGGTGGCCGGCGTCAGCGTT
CGCAGCCCGGCTCCGCGCAGGGCTCGGGCAAGCGGCCGCCACAGAAACAGTTTTTGCAGATCGTGCCGCG
AGGTGTCATGTTCGACGGTCAGACGGGGTTGATCAAGCATAAGACGGGACGGCTGCCTCTCATGTTCTAT
CGAGAGATTAAACATTTGTTGAGTCATGACATGGTTTGGCCGTGTCCTTGGCGCGAGACCCTGGTGGGTC
GCGTGGTGGGACCTATTCGTTTTCACACCTACGATCAGACGGACGCCGTGCTCTTCTTCGACTCGCCCGA
AAACGTGTCGCCGCGCTATCGTCAGCATCTGGTGCCTTCGGGGAACGTGTTGCGTTTCTTCGGGGCCACA
GAACACGGCTACAGTATCTGCGTCAACGTTTTCGGGCAGCGCAGCTACTTTTACTGTGAGTACAGCGACA
CCGATAGGCTGCGTGAGGTCATTGCCAGCGTGGGCGAACTAGTGCCCGAACCGCGGACGCCATACGCCGT
GTCTGTCACGCCGGCCACCAAGACCTCCATCTATGGGTACGGGACGCGACCCGTGCCCGATTTGCAGTGT

rpetit3

from urllib2 import Request, urlopen, URLError
import json
import math
import sys
import os
import socket
import optparse
​
def arg_parser():
 cwd_dir = os.getcwd()

rpetit3

#! /usr/bin/env bash
# https://www.ncbi.nlm.nih.gov/nuccore/1798174254
WUHAN=29903

while IFS=$'\t' read -r POSITION SAMPLE_ID ANALYSIS SEQUENCING_COVERAGE ASSEMBLY_COVERAGE; do
    if [ "${POSITION}" == "POSITION" ]; then
        printf "%s\t%s\t%s\t%s\t%s\n" "sample_id" "clearlabs_cov" "observed_cov" "mapped_coverage" "unmapped_coverage"
    else
        FASTQ=$(ls fastq/ | grep ${SAMPLE_ID})
        if [ -f "fastq/${FASTQ}" ]; then