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name: flye
channels:
- defaults
- anaconda
- bioconda
- conda-forge
dependencies:
- python=3.7
- flye=2.9.1
- seqkit=2.3.1
- blast=2.13.0
- nanoq=0.9.0 |
Run the following command to generate the ‘flye’ conda environment:
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conda activate flye |
merge FASTQ files
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cat FAU10290_pass_barcode96_0cf303ee_*.gz > merge_NC483.fastq.gz |
get path of merged file
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pwd |
modify launch*.pbs file
b) Run a de novo assembly and sequence comparison against a Reference genome
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#!/bin/bash -l
#PBS -N FlyeAssembly
#PBS -l walltime=24:00:00
#PBS -l mem=16gb
#PBS -l ncpus=8
## Usage: qsub launch_flye_genome_assembly.pbs
cd $PBS_O_WORKDIR
################################################################################################################################
# USER DEFINED VARIABLES
################################################################################################################################
SAMPLEID=MyGenome
REFNAME=Accession_RefGenome
REF='/path/to/REF/genome.fasta'
ONT='/path/to/ONT/reads.fastq.gz'
################################################################################################################################
#activate flye conda environment
conda activate flye
#STEP1: Run de novo genome assembly for >=Q20 data, use a combination of --nano-hq and --read-error 0.03
flye --out-dir outdir_nano --threads 8 --read-error 0.03 --nano-hq $ONT
#STEP2: Compare sequence similarity of assembled genome with reference sequence
blastn -query outdir_nano/assembly.fasta -subject $REF -evalue 1e-5 -out blastn_${REFNAME}_vs_${SAMPLEID}_assembly.txt -outfmt '6 qseqid sacc length pident mismatch gapopen qstart qend qlen sstart send slen evalue bitscore qcovhsp qcovs'
#STEP3: format output BLASTN table
echo "qseqid sacc length pident mismatch gapopen qstart qend qlen sstart send slen evalue bitscore qcovhsp qcovs" > header
#add header to blast output
cat header blastn_${REFNAME}_vs_${SAMPLEID}_assembly.txt > BLASTN_${REFNAME}_vs_${SAMPLEID}_assembly.txt
#remove intermediate files
rm header blastn_${REFNAME}_vs_${SAMPLEID}_assembly.txt
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submit the job
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qsub launch_flye_genome_assembly.pbs |
monitor progress of the assembly:
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