Supplementary File S1

#FastQC of raw reads
#v0.11.5

> mkdir fastqc_out
> fastqc *.fastq -o fastqc_out

#Trimmomatic 
#v0.39

> java -jar ~/Software/Trimmomatic-0.39/trimmomatic-0.39.jar PE -phred33 -threads 2 *_R1.fastq *_R2.fastq ILLUMINACLIP:TruSeq_PE_All.fa:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:4:25 MINLEN:50 2>&1 | tee trimomatic.log

#FastQC of trimmed reads 
#v0.11.5

> mkdir fastqctrim_out
> fastqc *_trimmed.fastq -o fastqctrim_out

#Join singles files 

> cat *_R1_singles.fastq *_R2_singles.fastq > *_singles.fastq

#SPAdes 
#v3.13.0

> spades.py -t 20 -o *_spades --pe1-1 *_R1_trimmed.fastq --pe1-2 *_R2_trimmed.fastq --pe1-s *_singles.fastq --cov-cutoff auto

#Filtering and renaming scaffolds (scaffolds >500bp, with coverage >3, ) 

> grep '>' scaffolds.fasta | awk -F "_" '$4>500 && $6>3 {print}' | sed 's/>//' > filtered.scaffold.id 
bioawk -cfastx 'BEGIN{while((getline k <"filtered.scaffold.id")>0)i[k]=1}{if(i[$name])print ">"$name"\n"$seq}' scaffolds.fasta > scaffolds_filtered.fasta

#QUAST
#v5.1

> quast.py -o Quast -t 4 scaffolds_filtered.fasta

#BUSCO
#v4.0.6 

> busco -i scaffolds_filtered.fasta -c 40 -o busco --out_path BUSCO -m geno --config /gitrepos/busco/config/config.ini -l fungi_odb10 --update-data
> busco -i scaffolds_filtered.fasta -c 40 -o busco --out_path BUSCO -m geno --config /gitrepos/busco/config/config.ini -l ascomycota_odb10 --update-data
> busco -i scaffolds_filtered.fasta -c 40 -o busco --out_path BUSCO -m geno --config /gitrepos/busco/config/config.ini -l sordariomycetes_odb10 --update-data

#AUGUSTUS
#v3.2.3

> augustus --species=fusarium_graminearum --genemodel=partial --gff3=on scaffolds_filtered.fasta > *.gff