Install FASTX-Toolkit using Conda conda install -c biobuilds fastx-toolkit=0.0.14

Convert FASTQ to FASTA

fastx-toolkit is not pair-aware, use seqtk instead

fastq_to_fasta -v -i infile.fastq -o outfile.fasta gunzip -c infile.fq.qc.gz | fastq_to_fasta -v -Q33 -o outfile.qc.fasta

Use AlignGraph AlignGraph –read1 reads_1.fa –read2 reads_2.fa –contig contigs.fa –genome genome.fa –distanceLow 100 –distanceHigh 1500 –extendedContig extendedContigs.fa –remainingContig remainingContigs.fa