Repository for the Microbiology Resource Announcements paper on five complete Streptococcus suis genomes

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mra_streptococcus_suis
mra_streptococcus_suis
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Repository for the Microbiology Resource Announcements paper on several closed Streptococcus suis genomes

Introduction

We sequenced 5 Streptococcus suis strains using Nanopore MinION sequencing technology. For these str

Code Snippets

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if [ -f $1 ]
then
	echo "Using $1 to get accession numbers"
else
	echo "Cannot access $1. Exiting..."
	exit 1
fi

NCOLS=$(awk '{print NF}' $1 | sort | uniq)

if [[ "$NCOLS" -eq 3 ]]
then
	echo "$1 contains three columns. Continuing..."
else
	echo "Please check if all rows of $1 contain three columns. Exiting..."
	exit 1
fi

echo "Will try to download data for $(($(wc -l $1 | awk '{print $1}') - 1)) samples"

awk 'NR>1 {print $0}' $1 | while read isolate illumina nanopore
do
	fasterq-dump ${illumina} --skip-technical -O raw_illumina
	mv raw_illumina/${illumina}_1.fastq raw_illumina/${isolate}_1.fastq
	mv raw_illumina/${illumina}_2.fastq raw_illumina/${isolate}_2.fastq
	gzip raw_illumina/${isolate}_1.fastq raw_illumina/${isolate}_2.fastq
	fasterq-dump ${nanopore} --skip-technical -O raw_nanopore
	mv raw_nanopore/${nanopore}.fastq raw_nanopore/${isolate}.fastq
	gzip raw_nanopore/${isolate}.fastq
done
Shell From line 3 of scripts/download_data.sh 
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seqtk comp $1 | awk '{gc += ($4 + $5)} {at += ($3 + $6)} END {print gc/(gc + at)}'
Shell seqtk From line 2 of scripts/get_gc.sh 
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shell:
	"""
	bash scripts/download_data.sh {input}
	"""
SnakeMake From line 35 of master/Snakefile 
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shell:
	"""
	fastp -w {threads} -z {params.compression_level} -i {input.fw} -o {output.fw} -I {input.rv} -O {output.rv} {params.general} --html {output.html} --json {output.json} 2>&1>{log}
	"""
SnakeMake fastp From line 57 of master/Snakefile 
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shell:
	"""
	filtlong --target_bases {params.target_bases} --illumina_1 {input.fw} --illumina_2 {input.rv} --trim {input.nanopore} | gzip > {output} 2>{log}
	"""
SnakeMake Filtlong From line 76 of master/Snakefile 
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shell:
	"""
	mkdir -p {output}
	fastqc -t {threads} --outdir {output} {input} 2>&1>{log}
	"""
SnakeMake FastQC From line 91 of master/Snakefile 
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shell:
	"""
	unicycler -1 {input.fw} -2 {input.rv} --long {input.nanopore} -o {params.outdir} --threads {threads}
	"""
SnakeMake Unicycler From line 111 of master/Snakefile 
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shell:
	"""
	quast -o {output} {input.assembly}
	"""
SnakeMake QUAST From line 125 of master/Snakefile 
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shell:
	"""
	mlst {input.assembly} 1> {output.mlst} 2>{log}
	"""
SnakeMake MLST From line 139 of master/Snakefile 
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shell:
	"""
	abricate --db {params.db} --mincov {params.mincov} --minid {params.minid} {input.assembly} 1> {output} 2>{log}
	"""
SnakeMake ABRicate From line 157 of master/Snakefile 
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shell:
	"""
	abricate --db {params.db} --mincov {params.mincov} --minid {params.minid} {input.assembly} 1> {output} 2>{log}
	"""
SnakeMake ABRicate From line 175 of master/Snakefile 
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shell:
	"""
	prokka {params.general} --force --compliant --centre XXX --outdir {output} --genus {params.genus} --species {params.species} --kingdom {params.kingdom} --cpus {threads} --prefix {params.prefix} {input.assembly} 2>&1>{log}
	if [ -f {output}/*.gff ]; then echo "{output} exists"; else exit 1; fi
	"""
SnakeMake metaprokka From line 196 of master/Snakefile 
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shell:
	"""
	minimap2 -a -x {params.minimap_x} -t {threads} {input.assembly} {input.fw} {input.rv} | samtools sort -l 0 --threads {threads} | bedtools genomecov -d -ibam stdin | awk '{{t += $3}} END {{print t/NR}}' 1>{output} 2>{log}
	"""
SnakeMake SAMtools BEDTools Minimap2 From line 216 of master/Snakefile 
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shell:
	"""
	minimap2 -a -x {params.minimap_x} -t {threads} {input.assembly} {input.reads} | samtools sort -l 0 --threads {threads} | bedtools genomecov -d -ibam stdin | awk '{{t += $3}} END {{print t/NR}}' 1>{output} 2>{log}
	"""
SnakeMake SAMtools BEDTools Minimap2 From line 234 of master/Snakefile 
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shell:
	"""
	bash scripts/get_gc.sh {input} > {output} 2>{log}
	"""
SnakeMake From line 248 of master/Snakefile
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Created: 1yr ago
Updated: 1yr ago
Maitainers: public
URL: https://github.com/boasvdp/MRA_Streptococcus_suis
Name: mra_streptococcus_suis
Version: 1
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Copyright: Public Domain
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