diff --git a/output_data/consensus-genomes/README.md b/output/consensus-genomes/README.md similarity index 100% rename from output_data/consensus-genomes/README.md rename to output/consensus-genomes/README.md diff --git a/output_data/consensus-genomes/VI1-minion-miseq-comparison-aln.fasta b/output/consensus-genomes/VI1-minion-miseq-comparison-aln.fasta similarity index 100% rename from output_data/consensus-genomes/VI1-minion-miseq-comparison-aln.fasta rename to output/consensus-genomes/VI1-minion-miseq-comparison-aln.fasta diff --git a/output_data/consensus-genomes/VI4-minion-miseq-comparison-aln.fasta b/output/consensus-genomes/VI4-minion-miseq-comparison-aln.fasta similarity index 100% rename from output_data/consensus-genomes/VI4-minion-miseq-comparison-aln.fasta rename to output/consensus-genomes/VI4-minion-miseq-comparison-aln.fasta diff --git a/output_data/consensus-genomes/ZIKA_USVI_good.fasta b/output/consensus-genomes/ZIKA_USVI_good.fasta similarity index 100% rename from output_data/consensus-genomes/ZIKA_USVI_good.fasta rename to output/consensus-genomes/ZIKA_USVI_good.fasta diff --git a/output_data/consensus-genomes/ZIKA_USVI_partial.fasta b/output/consensus-genomes/ZIKA_USVI_partial.fasta similarity index 100% rename from output_data/consensus-genomes/ZIKA_USVI_partial.fasta rename to output/consensus-genomes/ZIKA_USVI_partial.fasta diff --git a/output_data/consensus-genomes/ZIKA_USVI_poor.fasta b/output/consensus-genomes/ZIKA_USVI_poor.fasta similarity index 100% rename from output_data/consensus-genomes/ZIKA_USVI_poor.fasta rename to output/consensus-genomes/ZIKA_USVI_poor.fasta diff --git a/output_data/depth-coverage/README.md b/output/depth-coverage/README.md similarity index 100% rename from output_data/depth-coverage/README.md rename to output/depth-coverage/README.md diff --git a/output_data/depth-coverage/figures/usvi-library1/Coverage-Overlap-NB01-NB07.png b/output/depth-coverage/figures/usvi-library1/Coverage-Overlap-NB01-NB07.png similarity index 100% rename from output_data/depth-coverage/figures/usvi-library1/Coverage-Overlap-NB01-NB07.png rename to output/depth-coverage/figures/usvi-library1/Coverage-Overlap-NB01-NB07.png diff --git a/output_data/depth-coverage/figures/usvi-library1/Coverage-Overlap-NB02-NB08.png b/output/depth-coverage/figures/usvi-library1/Coverage-Overlap-NB02-NB08.png similarity index 100% rename from output_data/depth-coverage/figures/usvi-library1/Coverage-Overlap-NB02-NB08.png rename to output/depth-coverage/figures/usvi-library1/Coverage-Overlap-NB02-NB08.png diff --git a/output_data/depth-coverage/figures/usvi-library1/Coverage-Overlap-NB03-NB09.png b/output/depth-coverage/figures/usvi-library1/Coverage-Overlap-NB03-NB09.png similarity index 100% rename from output_data/depth-coverage/figures/usvi-library1/Coverage-Overlap-NB03-NB09.png rename to output/depth-coverage/figures/usvi-library1/Coverage-Overlap-NB03-NB09.png diff --git a/output_data/depth-coverage/figures/usvi-library1/Coverage-Overlap-NB04-NB10.png b/output/depth-coverage/figures/usvi-library1/Coverage-Overlap-NB04-NB10.png similarity index 100% rename from output_data/depth-coverage/figures/usvi-library1/Coverage-Overlap-NB04-NB10.png rename to output/depth-coverage/figures/usvi-library1/Coverage-Overlap-NB04-NB10.png diff --git a/output_data/depth-coverage/figures/usvi-library1/Coverage-Overlap-NB05-NB11.png b/output/depth-coverage/figures/usvi-library1/Coverage-Overlap-NB05-NB11.png similarity index 100% rename from output_data/depth-coverage/figures/usvi-library1/Coverage-Overlap-NB05-NB11.png rename to output/depth-coverage/figures/usvi-library1/Coverage-Overlap-NB05-NB11.png diff --git a/output_data/depth-coverage/figures/usvi-library1/Coverage-Overlap-NB06-NB12.png b/output/depth-coverage/figures/usvi-library1/Coverage-Overlap-NB06-NB12.png similarity index 100% rename from output_data/depth-coverage/figures/usvi-library1/Coverage-Overlap-NB06-NB12.png rename to output/depth-coverage/figures/usvi-library1/Coverage-Overlap-NB06-NB12.png diff --git a/output_data/depth-coverage/figures/usvi-library3/Coverage-Overlap-NB01-NB07.png b/output/depth-coverage/figures/usvi-library3/Coverage-Overlap-NB01-NB07.png similarity index 100% rename from output_data/depth-coverage/figures/usvi-library3/Coverage-Overlap-NB01-NB07.png rename to output/depth-coverage/figures/usvi-library3/Coverage-Overlap-NB01-NB07.png diff --git a/output_data/depth-coverage/figures/usvi-library3/Coverage-Overlap-NB02-NB08.png b/output/depth-coverage/figures/usvi-library3/Coverage-Overlap-NB02-NB08.png similarity index 100% rename from output_data/depth-coverage/figures/usvi-library3/Coverage-Overlap-NB02-NB08.png rename to output/depth-coverage/figures/usvi-library3/Coverage-Overlap-NB02-NB08.png diff --git a/output_data/depth-coverage/figures/usvi-library3/Coverage-Overlap-NB03-NB09.png b/output/depth-coverage/figures/usvi-library3/Coverage-Overlap-NB03-NB09.png similarity index 100% rename from output_data/depth-coverage/figures/usvi-library3/Coverage-Overlap-NB03-NB09.png rename to output/depth-coverage/figures/usvi-library3/Coverage-Overlap-NB03-NB09.png diff --git a/output_data/depth-coverage/figures/usvi-library3/Coverage-Overlap-NB04-NB10.png b/output/depth-coverage/figures/usvi-library3/Coverage-Overlap-NB04-NB10.png similarity index 100% rename from output_data/depth-coverage/figures/usvi-library3/Coverage-Overlap-NB04-NB10.png rename to output/depth-coverage/figures/usvi-library3/Coverage-Overlap-NB04-NB10.png diff --git a/output_data/depth-coverage/figures/usvi-library3/Coverage-Overlap-NB05-NB11.png b/output/depth-coverage/figures/usvi-library3/Coverage-Overlap-NB05-NB11.png similarity index 100% rename from output_data/depth-coverage/figures/usvi-library3/Coverage-Overlap-NB05-NB11.png rename to output/depth-coverage/figures/usvi-library3/Coverage-Overlap-NB05-NB11.png diff --git a/output_data/depth-coverage/figures/usvi-library3/Coverage-Overlap-NB06-NB12.png b/output/depth-coverage/figures/usvi-library3/Coverage-Overlap-NB06-NB12.png similarity index 100% rename from output_data/depth-coverage/figures/usvi-library3/Coverage-Overlap-NB06-NB12.png rename to output/depth-coverage/figures/usvi-library3/Coverage-Overlap-NB06-NB12.png diff --git a/output_data/depth-coverage/refs/ZikaReferenceGenome.fasta b/output/depth-coverage/refs/ZikaReferenceGenome.fasta similarity index 100% rename from output_data/depth-coverage/refs/ZikaReferenceGenome.fasta rename to output/depth-coverage/refs/ZikaReferenceGenome.fasta diff --git a/output_data/depth-coverage/refs/ZikaReferenceGenome.fasta.amb b/output/depth-coverage/refs/ZikaReferenceGenome.fasta.amb similarity index 100% rename from output_data/depth-coverage/refs/ZikaReferenceGenome.fasta.amb rename to output/depth-coverage/refs/ZikaReferenceGenome.fasta.amb diff --git a/output_data/depth-coverage/refs/ZikaReferenceGenome.fasta.ann b/output/depth-coverage/refs/ZikaReferenceGenome.fasta.ann similarity index 100% rename from output_data/depth-coverage/refs/ZikaReferenceGenome.fasta.ann rename to output/depth-coverage/refs/ZikaReferenceGenome.fasta.ann diff --git a/output_data/depth-coverage/refs/ZikaReferenceGenome.fasta.bwt b/output/depth-coverage/refs/ZikaReferenceGenome.fasta.bwt similarity index 100% rename from output_data/depth-coverage/refs/ZikaReferenceGenome.fasta.bwt rename to output/depth-coverage/refs/ZikaReferenceGenome.fasta.bwt diff --git a/output_data/depth-coverage/refs/ZikaReferenceGenome.fasta.pac b/output/depth-coverage/refs/ZikaReferenceGenome.fasta.pac similarity index 100% rename from output_data/depth-coverage/refs/ZikaReferenceGenome.fasta.pac rename to output/depth-coverage/refs/ZikaReferenceGenome.fasta.pac diff --git a/output_data/depth-coverage/refs/ZikaReferenceGenome.fasta.sa b/output/depth-coverage/refs/ZikaReferenceGenome.fasta.sa similarity index 100% rename from output_data/depth-coverage/refs/ZikaReferenceGenome.fasta.sa rename to output/depth-coverage/refs/ZikaReferenceGenome.fasta.sa