assemblycomparator2/LICENSE
assemblycomparator2/asscom2
assemblycomparator2/assets/checkm2_setup.py
assemblycomparator2/assets/ko00001.json
assemblycomparator2/assets/readme.txt
assemblycomparator2/conda_definitions/abricate.yaml
assemblycomparator2/conda_definitions/any2fasta.yaml
assemblycomparator2/conda_definitions/assembly-stats.yaml
assemblycomparator2/conda_definitions/bioawk.yaml
assemblycomparator2/conda_definitions/busco.yaml
assemblycomparator2/conda_definitions/checkm2.yaml
assemblycomparator2/conda_definitions/curl.yaml
assemblycomparator2/conda_definitions/dbcan.yaml
assemblycomparator2/conda_definitions/diamond.yaml
assemblycomparator2/conda_definitions/fasttree.yaml
assemblycomparator2/conda_definitions/gtdbtk.yaml
assemblycomparator2/conda_definitions/inactive/checkm copy.yaml
assemblycomparator2/conda_definitions/inactive/checkm.yaml
assemblycomparator2/conda_definitions/inactive/checkm2.yaml
assemblycomparator2/conda_definitions/inactive/py_3_7_tools.yaml
assemblycomparator2/conda_definitions/inactive/py_3_8_tools.yaml
assemblycomparator2/conda_definitions/inactive/roary2.yaml
assemblycomparator2/conda_definitions/inactive/roary_old.yaml
assemblycomparator2/conda_definitions/inactive/wget.yaml
assemblycomparator2/conda_definitions/interproscan.yaml
assemblycomparator2/conda_definitions/kofam_scan.yaml
assemblycomparator2/conda_definitions/kraken2.yaml
assemblycomparator2/conda_definitions/limbo/checkm2.yaml
assemblycomparator2/conda_definitions/limbo/r-tidyverse.yaml
assemblycomparator2/conda_definitions/limbo/roary.yaml
assemblycomparator2/conda_definitions/limbo/roary_old.yaml
assemblycomparator2/conda_definitions/limbo/wget.yaml
assemblycomparator2/conda_definitions/mashtree.yaml
assemblycomparator2/conda_definitions/mlst.yaml
assemblycomparator2/conda_definitions/prokka.yaml
assemblycomparator2/conda_definitions/r-clusterProfiler.yaml
assemblycomparator2/conda_definitions/roary_see-comments-in-this-file.yaml
assemblycomparator2/conda_definitions/seqkit.yaml
assemblycomparator2/conda_definitions/sketch.txt.sh
assemblycomparator2/conda_definitions/snp-dists.yaml
assemblycomparator2/config.yaml
assemblycomparator2/profiles/apptainer/local/config.yaml
assemblycomparator2/profiles/apptainer/pbs-qut-lyra/config.yaml
assemblycomparator2/profiles/apptainer/slurm-au-genomedk/config.yaml
assemblycomparator2/profiles/apptainer/slurm-nmbu-orion/config.yaml
assemblycomparator2/profiles/apptainer/slurm-sigma2-saga/config.yaml
assemblycomparator2/profiles/conda/local/config.yaml
assemblycomparator2/profiles/conda/pbs-qut-lyra/config.yaml
assemblycomparator2/profiles/conda/slurm-au-genomedk/config.yaml
assemblycomparator2/profiles/conda/slurm-nmbu-orion/config.yaml
assemblycomparator2/profiles/conda/slurm-sigma2-saga/config.yaml
assemblycomparator2/report_subpipeline/conda_definitions/r-markdown.yaml
assemblycomparator2/report_subpipeline/scripts/_report_end_script.sh
assemblycomparator2/report_subpipeline/scripts/genomes_to_report_v2.Rmd
assemblycomparator2/report_subpipeline/scripts/genomes_to_report_v3.Rmd
assemblycomparator2/report_subpipeline/scripts/report_section_A.rmd
assemblycomparator2/report_subpipeline/scripts/section_abricate.rmd
assemblycomparator2/report_subpipeline/scripts/section_assembly_stats.rmd
assemblycomparator2/report_subpipeline/scripts/section_busco.rmd
assemblycomparator2/report_subpipeline/scripts/section_checkm2.rmd
assemblycomparator2/report_subpipeline/scripts/section_gtdbtk.rmd
assemblycomparator2/report_subpipeline/scripts/section_kegg_pathway.rmd
assemblycomparator2/report_subpipeline/scripts/section_kraken2.rmd
assemblycomparator2/report_subpipeline/scripts/section_mashtree.rmd
assemblycomparator2/report_subpipeline/scripts/section_mlst.rmd
assemblycomparator2/report_subpipeline/scripts/section_prokka.rmd
assemblycomparator2/report_subpipeline/scripts/section_roary.rmd
assemblycomparator2/report_subpipeline/scripts/section_sequence_lengths.rmd
assemblycomparator2/report_subpipeline/scripts/section_snp_dists.rmd
assemblycomparator2/report_subpipeline/snakefile
assemblycomparator2/scripts/inactive/download_setup_checkm.sh
assemblycomparator2/scripts/inactive/genomes_to_report_v3.Rmd
assemblycomparator2/scripts/inactive/genomes_to_reportv1.Rmd
assemblycomparator2/scripts/inactive/genomic_gc_old.r
assemblycomparator2/scripts/inactive/set-up-kraken2_PlusPF_50GB.sh
assemblycomparator2/scripts/inactive/set-up-kraken2_Standard_8GB.sh
assemblycomparator2/scripts/inactive/shell_extensions.sh
assemblycomparator2/scripts/kegg_pathway_enrichment_analysis.R
assemblycomparator2/snakefile
assemblycomparator2/tests/E._faecium/116_2.fna
assemblycomparator2/tests/E._faecium/E8202.fna
assemblycomparator2/tests/E._faecium/SRR24.fna
assemblycomparator2/tests/E._faecium_30/GCF_000764975.1_ASM76497v1_genomic.fna
assemblycomparator2/tests/E._faecium_30/GCF_000764985.1_ASM76498v1_genomic.fna
assemblycomparator2/tests/E._faecium_30/GCF_000767345.1_ASM76734v1_genomic.fna
assemblycomparator2/tests/E._faecium_30/GCF_000767365.1_ASM76736v1_genomic.fna
assemblycomparator2/tests/E._faecium_30/GCF_000772505.1_ASM77250v1_genomic.fna
assemblycomparator2/tests/E._faecium_30/GCF_000772525.1_ASM77252v1_genomic.fna
assemblycomparator2/tests/E._faecium_30/GCF_000787055.1_ASM78705v1_genomic.fna
assemblycomparator2/tests/E._faecium_30/GCF_000787065.1_ASM78706v1_genomic.fna
assemblycomparator2/tests/E._faecium_30/GCF_000804385.1_70-61-7_genomic.fna
assemblycomparator2/tests/E._faecium_30/GCF_000804405.1_ASM80440v1_genomic.fna
assemblycomparator2/tests/E._faecium_30/GCF_000804415.1_70-8-2_genomic.fna
assemblycomparator2/tests/E._faecium_30/GCF_000934365.1_ASM93436v1_genomic.fna
assemblycomparator2/tests/E._faecium_30/GCF_000951815.1_ASM95181v1_genomic.fna
assemblycomparator2/tests/E._faecium_30/GCF_001005615.1_ASM100561v1_genomic.fna
assemblycomparator2/tests/E._faecium_30/GCF_001025245.1_ASM102524v1_genomic.fna
assemblycomparator2/tests/E._faecium_30/GCF_001025255.1_ASM102525v1_genomic.fna
assemblycomparator2/tests/E._faecium_30/GCF_001025265.1_ASM102526v1_genomic.fna
assemblycomparator2/tests/E._faecium_30/GCF_001025315.1_ASM102531v1_genomic.fna
assemblycomparator2/tests/E._faecium_30/GCF_001025325.1_ASM102532v1_genomic.fna
assemblycomparator2/tests/E._faecium_30/GCF_001025335.1_ASM102533v1_genomic.fna
assemblycomparator2/tests/E._faecium_30/GCF_001025375.1_ASM102537v1_genomic.fna
assemblycomparator2/tests/E._faecium_30/GCF_001025385.1_ASM102538v1_genomic.fna
assemblycomparator2/tests/E._faecium_30/GCF_001025405.1_ASM102540v1_genomic.fna
assemblycomparator2/tests/E._faecium_30/GCF_001025435.1_ASM102543v1_genomic.fna
assemblycomparator2/tests/E._faecium_30/GCF_001039515.1_ASM103951v1_genomic.fna
assemblycomparator2/tests/E._faecium_30/GCF_001052395.1_ASM105239v1_genomic.fna
assemblycomparator2/tests/E._faecium_30/GCF_001052405.1_ASM105240v1_genomic.fna
assemblycomparator2/tests/E._faecium_30/GCF_001052435.1_ASM105243v1_genomic.fna
assemblycomparator2/tests/E._faecium_30/GCF_001052485.1_ASM105248v1_genomic.fna
assemblycomparator2/tests/E._faecium_30/GCF_009734005.1_ASM973400v2_genomic.fna
assemblycomparator2/tests/E._faecium_plasmids/116_2.fna
assemblycomparator2/tests/E._faecium_plasmids/Dallas_55.fna
assemblycomparator2/tests/E._faecium_plasmids/E8202.fna
assemblycomparator2/tests/E._faecium_plasmids/EF_VRE.fna
assemblycomparator2/tests/E._faecium_plasmids/ISMMS_VRE_1.fna
assemblycomparator2/tests/E._faecium_plasmids/VB3240.fna
assemblycomparator2/tests/E._faecium_plasmids/report_E._faecium_plasmids.html.zip
assemblycomparator2/tests/MAGs/Treatment_LowE.metabat.242.fasta
assemblycomparator2/tests/MAGs/Treatment_LowE.metabat.461.fasta
assemblycomparator2/tests/MAGs/Treatment_LowE.metabat.618.fasta
assemblycomparator2/tests/MAGs/Treatment_MidE.metabat.482.fasta
assemblycomparator2/tests/strachan_campylo/GCF_027736965.1_ASM2773696v1_genomic.fna
assemblycomparator2/tests/strachan_campylo/GCF_027736975.1_ASM2773697v1_genomic.fna
assemblycomparator2/tests/strachan_campylo/GCF_027736985.1_ASM2773698v1_genomic.fna
assemblycomparator2/tests/strachan_campylo/GCF_027737105.1_ASM2773710v1_genomic.fna
assemblycomparator2/tests/strachan_campylo/GCF_027737145.1_ASM2773714v1_genomic.fna
assemblycomparator2/tests/strachan_campylo/GCF_027737225.1_ASM2773722v1_genomic.fna
assemblycomparator2/tests/strachan_campylo/GCF_027737245.1_ASM2773724v1_genomic.fna
assemblycomparator2/tests/strachan_campylo/GCF_027737305.1_ASM2773730v1_genomic.fna
assemblycomparator2/tests/strachan_campylo/GCF_027737365.1_ASM2773736v1_genomic.fna
assemblycomparator2/tests/strachan_campylo/GCF_027737405.1_ASM2773740v1_genomic.fna
assemblycomparator2/tests/strachan_campylo/GCF_027737445.1_ASM2773744v1_genomic.fna
assemblycomparator2/tests/strachan_campylo/GCF_027737485.1_ASM2773748v1_genomic.fna
assemblycomparator2/tests/strachan_campylo/GCF_027737535.1_ASM2773753v1_genomic.fna
assemblycomparator2/tests/strachan_campylo/GCF_027737585.1_ASM2773758v1_genomic.fna
assemblycomparator2/tests/strachan_campylo/GCF_027737625.1_ASM2773762v1_genomic.fna
assemblycomparator2/tests/strachan_campylo/GCF_027737645.1_ASM2773764v1_genomic.fna
assemblycomparator2/tests/strachan_campylo/GCF_027737655.1_ASM2773765v1_genomic.fna
assemblycomparator2/tests/strachan_campylo/GCF_027737785.1_ASM2773778v1_genomic.fna
assemblycomparator2/tests/strachan_campylo/GCF_027737825.1_ASM2773782v1_genomic.fna
assemblycomparator2/tests/strachan_campylo/GCF_027737865.1_ASM2773786v1_genomic.fna
assemblycomparator2/tests/strachan_campylo/GCF_027737875.1_ASM2773787v1_genomic.fna
assemblycomparator2/tests/strachan_campylo/GCF_027737945.1_ASM2773794v1_genomic.fna
assemblycomparator2/tests/strachan_campylo/GCF_027737985.1_ASM2773798v1_genomic.fna
assemblycomparator2/tests/strachan_campylo/GCF_027738065.1_ASM2773806v1_genomic.fna
assemblycomparator2/tests/strachan_campylo/GCF_027738075.1_ASM2773807v1_genomic.fna
assemblycomparator2/tests/strachan_campylo/GCF_027738125.1_ASM2773812v1_genomic.fna
assemblycomparator2/tests/strachan_campylo/GCF_027738185.1_ASM2773818v1_genomic.fna
assemblycomparator2/tests/strachan_campylo/GCF_027738265.1_ASM2773826v1_genomic.fna
assemblycomparator2/tests/strachan_campylo/GCF_027738295.1_ASM2773829v1_genomic.fna
assemblycomparator2/tests/strachan_campylo/GCF_027738315.1_ASM2773831v1_genomic.fna
assemblycomparator2/tests/strachan_campylo/GCF_027738385.1_ASM2773838v1_genomic.fna
assemblycomparator2/tests/strachan_campylo/GCF_027797205.1_ASM2779720v1_genomic.fna
assemblycomparator2/tests/strachan_campylo/GCF_027797465.1_ASM2779746v1_genomic.fna
assemblycomparator2/tests/strachan_campylo/GCF_027797495.1_ASM2779749v1_genomic.fna
assemblycomparator2/tests/strachan_campylo/report_strachan_campylo.html.zip
assemblycomparator2/tests/test.sh
bin/asscom2
