ENA SARS-CoV-2 Nanopore Amplicon Sequencing Analysis Workflow

public public 1yr ago Version: Version 1 0 bookmarks
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ena-sars-cov-2-nanopore-amplicon-sequencing-analys
ena-sars-cov-2-nanopore-amplicon-sequencing-analys
ena-sars-cov-2-nanopore-amplicon-sequencing-analys
ena-sars-cov-2-nanopore-amplicon-sequencing-analys
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Pipeline for mapping SARS-CoV2 nanopore reads using nextflow

Code Snippets

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"""
cutadapt -u 30 -u -30 -o trimmed.fastq ${input_file} -m 75 -j ${task.cpus} --quiet
"""
NextFlow Cutadapt From line 28 of master/nanopore_nextflow.nf 
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"""
minimap2 -Y -t ${task.cpus} -x map-ont -a ${ref} ${trimmed} | samtools view -bF 4 - | samtools sort -@ ${task.cpus} - > ${run_id}.bam
"""
NextFlow SAMtools Minimap2 From line 53 of master/nanopore_nextflow.nf 
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"""
samtools mpileup -a -A -Q 0 -d 8000 -f ${sars2_fasta} ${bam} > \
${run_id}.pileup
"""
NextFlow SAMtools From line 74 of master/nanopore_nextflow.nf 
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"""
cat ${pileup} | awk '{print \$2,","\$3,","\$4}' > ${run_id}.coverage
"""
NextFlow From line 95 of master/nanopore_nextflow.nf 
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"""
samtools index -@ ${task.cpus} ${bam}
bam_to_vcf.py -b ${bam} -r ${ref} --mindepth 30 --minAF 0.1 -c ${task.cpus} -o ${run_id}.vcf
filtervcf.py -i ${run_id}.vcf -o ${run_id}_filtered.vcf
bgzip ${run_id}.vcf
bgzip ${run_id}_filtered.vcf
"""
NextFlow SAMtools From line 118 of master/nanopore_nextflow.nf 
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"""
zcat ${vcf} | sed "s/^NC_045512.2/NC_045512/" > \
${run_id}.newchr.vcf
java -Xmx4g -jar /data/tools/snpEff/snpEff.jar -q -no-downstream -no-upstream -noStats sars.cov.2 ${run_id}.newchr.vcf > ${run_id}.annot.vcf
"""
NextFlow From line 141 of master/nanopore_nextflow.nf 
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"""
tabix ${vcf}
vcf2consensus.py -v ${vcf} -d ${coverage} -r ${sars2_fasta} -o ${run_id}_consensus.fasta -dp 30 -n ${run_id}
bgzip ${run_id}_consensus.fasta
"""
NextFlow tabix From line 165 of master/nanopore_nextflow.nf
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Created: 1yr ago
Updated: 1yr ago
Maitainers: public
URL: https://github.com/dnieuw/ENA_SARS_Cov2_nanopore
Name: ena-sars-cov-2-nanopore-amplicon-sequencing-analys
Version: Version 1
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Copyright: Public Domain
License: GNU General Public License v3.0
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