python-scripts/MoGAAAP
site-packages/MoGAAAP/MoGAAAP.py
site-packages/MoGAAAP/__init__.py
site-packages/MoGAAAP/config/.gitignore
site-packages/MoGAAAP/config/example.tsv
site-packages/MoGAAAP/config/example.yaml
site-packages/MoGAAAP/config/examples/HOX.amac
site-packages/MoGAAAP/config/examples/NBS_HMM.amac
site-packages/MoGAAAP/config/examples/arabidopsis.tsv
site-packages/MoGAAAP/config/examples/arabidopsis.yaml
site-packages/MoGAAAP/config/examples/grape.tsv
site-packages/MoGAAAP/config/examples/grape.yaml
site-packages/MoGAAAP/config/examples/human.tsv
site-packages/MoGAAAP/config/examples/human.yaml
site-packages/MoGAAAP/utils.py
site-packages/MoGAAAP/workflow/Snakefile
site-packages/MoGAAAP/workflow/envs/agat.yaml
site-packages/MoGAAAP/workflow/envs/bedtools.yaml
site-packages/MoGAAAP/workflow/envs/bioawk.yaml
site-packages/MoGAAAP/workflow/envs/blast.yaml
site-packages/MoGAAAP/workflow/envs/busco.yaml
site-packages/MoGAAAP/workflow/envs/circos.yaml
site-packages/MoGAAAP/workflow/envs/csvtotable.yaml
site-packages/MoGAAAP/workflow/envs/flye.yaml
site-packages/MoGAAAP/workflow/envs/hifiasm.yaml
site-packages/MoGAAAP/workflow/envs/kraken2.post-deploy.sh
site-packages/MoGAAAP/workflow/envs/kraken2.yaml
site-packages/MoGAAAP/workflow/envs/liftoff.yaml
site-packages/MoGAAAP/workflow/envs/mapping.yaml
site-packages/MoGAAAP/workflow/envs/mashmap.yaml
site-packages/MoGAAAP/workflow/envs/merqury.yaml
site-packages/MoGAAAP/workflow/envs/minimap2.yaml
site-packages/MoGAAAP/workflow/envs/multiqc.yaml
site-packages/MoGAAAP/workflow/envs/ntjoin.yaml
site-packages/MoGAAAP/workflow/envs/ntsynt.yaml
site-packages/MoGAAAP/workflow/envs/oma.post-deploy.sh
site-packages/MoGAAAP/workflow/envs/oma.yaml
site-packages/MoGAAAP/workflow/envs/pantools.yaml
site-packages/MoGAAAP/workflow/envs/ragtag.yaml
site-packages/MoGAAAP/workflow/envs/rbase.yaml
site-packages/MoGAAAP/workflow/envs/samtools.yaml
site-packages/MoGAAAP/workflow/envs/seqkit.yaml
site-packages/MoGAAAP/workflow/envs/seqtk.yaml
site-packages/MoGAAAP/workflow/envs/verkko.yaml
site-packages/MoGAAAP/workflow/envs/yahs.yaml
site-packages/MoGAAAP/workflow/profiles/default/config.yaml
site-packages/MoGAAAP/workflow/report/blast.rst
site-packages/MoGAAAP/workflow/report/busco.rst
site-packages/MoGAAAP/workflow/report/circos_overview.rst
site-packages/MoGAAAP/workflow/report/circos_plot.rst
site-packages/MoGAAAP/workflow/report/fcs-adaptor.rst
site-packages/MoGAAAP/workflow/report/fcs-gx.rst
site-packages/MoGAAAP/workflow/report/hic.rst
site-packages/MoGAAAP/workflow/report/kmer-db.rst
site-packages/MoGAAAP/workflow/report/kraken.rst
site-packages/MoGAAAP/workflow/report/mapping.rst
site-packages/MoGAAAP/workflow/report/mash.rst
site-packages/MoGAAAP/workflow/report/merqury_plot.rst
site-packages/MoGAAAP/workflow/report/merqury_qv.rst
site-packages/MoGAAAP/workflow/report/mummerplot.rst
site-packages/MoGAAAP/workflow/report/ntsynt.rst
site-packages/MoGAAAP/workflow/report/omark.rst
site-packages/MoGAAAP/workflow/report/pangrowth_core.rst
site-packages/MoGAAAP/workflow/report/pangrowth_growth.rst
site-packages/MoGAAAP/workflow/report/pangrowth_hist.rst
site-packages/MoGAAAP/workflow/report/pantools_core_accessory_unique.rst
site-packages/MoGAAAP/workflow/report/pantools_core_dispensable.rst
site-packages/MoGAAAP/workflow/report/pantools_core_dispensable_total.rst
site-packages/MoGAAAP/workflow/report/pantools_upset.rst
site-packages/MoGAAAP/workflow/report/sans.rst
site-packages/MoGAAAP/workflow/report/statistics.rst
site-packages/MoGAAAP/workflow/report/telo.rst
site-packages/MoGAAAP/workflow/report/workflow.rst
site-packages/MoGAAAP/workflow/rules/1.assembly/01.assembly.smk
site-packages/MoGAAAP/workflow/rules/1.assembly/02.contigs.smk
site-packages/MoGAAAP/workflow/rules/1.assembly/03.mummer.smk
site-packages/MoGAAAP/workflow/rules/1.assembly/04.scaffolding.smk
site-packages/MoGAAAP/workflow/rules/1.assembly/05.renaming.smk
site-packages/MoGAAAP/workflow/rules/1.assembly/06.mummer.smk
site-packages/MoGAAAP/workflow/rules/1.assembly/all.smk
site-packages/MoGAAAP/workflow/rules/2.annotation/01.liftoff.smk
site-packages/MoGAAAP/workflow/rules/2.annotation/02.helixer.smk
site-packages/MoGAAAP/workflow/rules/2.annotation/03.combined.smk
site-packages/MoGAAAP/workflow/rules/2.annotation/04.asm_bed.smk
site-packages/MoGAAAP/workflow/rules/2.annotation/05.blastdb.smk
site-packages/MoGAAAP/workflow/rules/2.annotation/06.blast_p.smk
site-packages/MoGAAAP/workflow/rules/2.annotation/07.blast_n.smk
site-packages/MoGAAAP/workflow/rules/2.annotation/08.blp2bed.smk
site-packages/MoGAAAP/workflow/rules/2.annotation/09.bln2bed.smk
site-packages/MoGAAAP/workflow/rules/2.annotation/10.bcovblp.smk
site-packages/MoGAAAP/workflow/rules/2.annotation/11.bcovbln.smk
site-packages/MoGAAAP/workflow/rules/2.annotation/12.circos.smk
site-packages/MoGAAAP/workflow/rules/2.annotation/13.separate_genome.smk
site-packages/MoGAAAP/workflow/rules/2.annotation/14.telo.smk
site-packages/MoGAAAP/workflow/rules/2.annotation/all.smk
site-packages/MoGAAAP/workflow/rules/3.quality_assessment/00.proteome.smk
site-packages/MoGAAAP/workflow/rules/3.quality_assessment/01.merqury.smk
site-packages/MoGAAAP/workflow/rules/3.quality_assessment/02.kraken.smk
site-packages/MoGAAAP/workflow/rules/3.quality_assessment/03.fcs.smk
site-packages/MoGAAAP/workflow/rules/3.quality_assessment/04.mapping.smk
site-packages/MoGAAAP/workflow/rules/3.quality_assessment/05.pantools.smk
site-packages/MoGAAAP/workflow/rules/3.quality_assessment/06.busco.smk
site-packages/MoGAAAP/workflow/rules/3.quality_assessment/07.omark.smk
site-packages/MoGAAAP/workflow/rules/3.quality_assessment/09.mash.smk
site-packages/MoGAAAP/workflow/rules/3.quality_assessment/10.ntsynt.smk
site-packages/MoGAAAP/workflow/rules/3.quality_assessment/11.sans.smk
site-packages/MoGAAAP/workflow/rules/3.quality_assessment/12.pangrowth.smk
site-packages/MoGAAAP/workflow/rules/3.quality_assessment/13.statistics.smk
site-packages/MoGAAAP/workflow/rules/3.quality_assessment/all.smk
site-packages/MoGAAAP/workflow/rules/agat.smk
site-packages/MoGAAAP/workflow/rules/common.smk
site-packages/MoGAAAP/workflow/schemas/config.schema.yaml
site-packages/MoGAAAP/workflow/schemas/samples.schema.yaml
site-packages/MoGAAAP/workflow/scripts/OMArk.a3c75ad/plot_all_results.py
site-packages/MoGAAAP/workflow/scripts/create_circos_config.py
site-packages/MoGAAAP/workflow/scripts/make_subrange_from_bed.py
site-packages/MoGAAAP/workflow/scripts/merge_tsv_files.sh
site-packages/MoGAAAP/workflow/scripts/pheatmap_lower_triangle.R
site-packages/MoGAAAP/workflow/scripts/renaming_scaffolds.py
site-packages/MoGAAAP/workflow/scripts/tcl_blast2bed_converter.tcl
site-packages/MoGAAAP/workflow/singularity/haphic/haphic.f8f7451.def
site-packages/MoGAAAP/workflow/singularity/mummer/mummer-4.0.0rc1.def
site-packages/MoGAAAP/workflow/singularity/ntSynt/ntSynt-viz.v1.0.0.def
site-packages/MoGAAAP/workflow/singularity/pangrowth/pangrowth.71d67bde89326644f6718c82ec2ee7b751f3080b.def
site-packages/MoGAAAP/workflow/singularity/sans/sans.v1.0.0.def
site-packages/mogaaap-1.2.0.dist-info/INSTALLER
site-packages/mogaaap-1.2.0.dist-info/METADATA
site-packages/mogaaap-1.2.0.dist-info/RECORD
site-packages/mogaaap-1.2.0.dist-info/REQUESTED
site-packages/mogaaap-1.2.0.dist-info/WHEEL
site-packages/mogaaap-1.2.0.dist-info/direct_url.json
site-packages/mogaaap-1.2.0.dist-info/entry_points.txt
site-packages/mogaaap-1.2.0.dist-info/licenses/LICENSE
