02b_scripts.md

Scripts used to run the analysis

Quallity control

Running all barcodes in a loop

for n in 4 5 6 7 8 9 ; do   nextflow run /work/gif/Maryam/Programfiles/nanoQCtrim/main.nf --fastqs ../00-RawData/barcode1$n/combine-barcode1$n.fastq   --outdir output-barcode1$n  --options '-middle_threshold 100' -profile nova,singularity; done

where

• main.nf

Assembly of each line with Flye genome assembler

Runing flye

for n in 4 5 6 7 8 9 ; do
flye --nano-raw /work/gif/Maryam/projects/Zengyi-2021-ScheffersomycesStipitis/01-QC/output-barcode$n/trimmedReads/FAO68114_pass_barcode$n_598c81f2_0_adaptersRemoved.fastq --out-dir out_barcode$n
 --genome-size 15m --threads 30 -i 4

Alignment

Aligning the inserts on the assemblies with minimap2

for n in 4 5 6 7 8 9 ; do
minimap2 -aLx map-ont  /work/gif/Maryam/projects/Zengyi-2021-ScheffersomycesStipitis/00-RawData/inserts-all.fasta  /work/gif/Maryam/projects/Zengyi-2021-ScheffersomycesStipitis/02-fly/out_
flye_b$n/assembly.fasta  > aln-b$n\.sam " >> minimap2_$n

Selecting 10K bp upstream from the insert location on each assembly

We used samtools to extract 10kb upstream sections of the assembly for each insert location. We aligned back these sections on the reference genome to estimate the insert locations on the reference genome.

Aligning the 10kb upstream (from the insert location) sections of the assemblies on the reference genome with minimap2

for n in 4 5 6 7 8 9 ; do
minimap2 -aLx map-ont  /work/gif/Maryam/projects/Zengyi-2021-ScheffersomycesStipitis/03-alignment/uniq-alignemnt/GCA_006942115.1_ASM694211v1_genomic.fna  inserts$n-minimap.fasta > aln$n.sam

From the sam files we can estimate the insert locations on the reference genome.