NOTE: Use the NextFlow: ONTprocessing pipeline instead of this guide to process Oxford Nanopore data collected for viruses (i.e., insects).
Source:
https://github.com/PrestonLeung/Nano-Q
Create a conda environment:
Prepare an “environment.yml” file that contains the following tool specifications
| Code Block |
|---|
name: nanoQ channels: - defaults - anaconda - bioconda - conda-forge dependencies: - python=3.7 - pysam=0.19.1 - numpy=1.23.3 - scipy=1.9.1 - biophytonbiopython=1.79 - matplotlib=3.6.0 - samtools - minimap2 - graphmap - emboss |
...
| Code Block |
|---|
#!/bin/bash -l #PBS -N nano-Q #PBS -l walltime=24:00:00 #PBS -l mem=16gb #PBS -l ncpus=8 cd $PBS_O_WORKDIR ################################################################################################################################ # USER DEFINE VARIABLES ################################################################################################################################ SAMPLEID=NC483 REFNAME=NC001477_RefGenome LIST='/workmyteam/phylo/OxfordNanopore/nextflow/assembly/data/NC483/NC483_NC001477_ref_list.txt' REF='/workmyteam/phylo/OxfordNanopore/nextflow/assembly/data/NC483/NC483_NC001477_reference_sequence.fasta' ONT='/workmyteam/phylo/OxfordNanopore/nextflow/assembly/data/NC483/NC483_FAU10290_pass_barcode96_0cf303ee.fastq' ################################################################################################################################ #activate conda environment containing tools for analysis conda activate nanoQ2 #generic mapping reads minimap2 -a $REF $ONT > ${SAMPLEID}_aln.sam #mapping noisy reads #minimap2 -ax $REF $ONT > ${SAMPLEID}_aln2.sam #Samtools samtools view -bt ${LIST} -o ${SAMPLEID}_aln.bam ${SAMPLEID}_aln.sam samtools sort -T /tmp/aln.sorted -o ${SAMPLEID}_aln.sorted.bam ${SAMPLEID}_aln.bam samtools index ${SAMPLEID}_aln.sorted.bam #run nano-Q python /work/phylo/OxfordNanopore/nextflow/tools/git/Nano-Q/nano-q.py -b ${SAMPLEID}_aln.sorted.bam -c 1 -l 9000 -nr 1 -q 5 -j 10 |
creating a ref_list.txt file
| Code Block |
|---|
#use a tool provided by emboss
infoseq $REF -only -name -length | sed 1d > ${REF}_list.txt |
submit the job to the scheduler
...
| Code Block |
|---|
/work/phylo/OxfordNanopore/nextflow/variants/nano-Q/run2 |
Additional information
| Code Block |
|---|
#generic mapping reads minimap2 -a ref.fa ont-reads.fq > aln.sam #mapping noisy reads minimap2 -ax map-ont ref.fa ont-reads.fq > aln.sam # for Oxford Nanopore reads |
Full genome/assembly alignment
| Code Block |
|---|
minimap2 -ax asm5 ref.fa asm.fa > aln.sam # assembly to assembly/ref alignment |
...