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Evaluate a genome assembly

0 results • updated 18 months ago by Istvan Albert • needs authorization

Evaluate a genome assembly

In the paper titled: "A pneumonia outbreak associated with a new coronavirus of probable bat origin"

https://www.nature.com/articles/s41586-020-2012-7

the authors have assembled the bat coronavirus that is most similar to SARS-COV-2.

Evaluate that claim by investigating how well the sequencing data deposited for the new organism aligns with the novel bat genome that they have discovered. The data can be obtained from Genbank and SRA.

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# Reference genome accession number.
ACC=MN996532

# The SRR number for the sequencing data.
SRR=SRR11085797

# Alignment file.
BAM=${SRR}-${ACC}.bam

# Readcount
N=10000

# The name for the read pairs.
R1=reads/${SRR}_1.fastq
R2=reads/${SRR}_2.fastq

# The reference genome stored locally.
REF=refs/${ACC}.fa

genome:
	mkdir -p refs
	bio fetch -format fasta ${ACC} > ${REF}
	samtools faidx ${REF}
	bwa index ${REF}

data:
	# Obtain the FASTQ sequences for the SRR number.
	mkdir -p reads
	fastq-dump -F -X ${N} --split-files ${SRR} -O reads

align:
	# Run the bwa aligner. 
	bwa mem -t 4 ${REF} ${R1} ${R2} | samtools sort > ${BAM}
	samtools index ${BAM}
	samtools flagstat ${BAM} > report.txt
	cat report.txt

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Evaluate an assembly

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