BBtools Guide Check for contamination sendsketch.sh in= ../4_8.fastq Remove contamination via gc content bbduk.sh in1=Z001_illumina_1.pe.qc.fastq in2=Z001_illumina_2.pe.qc.fastq out1=clean_Z001_illumina_1.fastq\ out2=clean_Z001_illumina_2.fastq mingc=0.45 Remove contamination via mapping reads to genomes bbsplit.sh in1=./raw_reads/DMS92_2_S159_R1_001.fastq.gz in2=./raw_reads/DMS92_2_S159_R2_001.fastq.gz\ ref=/media/danimstevens/Second_storage/Genomes/DNA_contigs/CM_CASJ002.fasta,./GCF_000725365.1.fa.gz,\ ./GCF_900110015.1.fa.gz basename=out_%.fq outu1=clean1.fq outu2=clean2.fq Determining read coverage bbmap.sh in=reads.fq ref=contigs.fa covstats=covstats.txt Removing small (<1kb) contigs reformat.sh in=contigs.fasta out=filtered.fasta minlength=1000