Python Module Index

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neatseq_flow_modules
    neatseq_flow_modules.Annotation.prokka_old
    neatseq_flow_modules.Assembly.clc_assembl
    neatseq_flow_modules.Assembly.megahit_assembl
    neatseq_flow_modules.ChIP_seq.CEAS
    neatseq_flow_modules.ChIP_seq.macs2_bdgcmp
    neatseq_flow_modules.clustering.cd_hit
    neatseq_flow_modules.clustering.vsearch_cluster
    neatseq_flow_modules.clustering.vsearch_derepel
    neatseq_flow_modules.GATK_modules.CNV_per_Exon
    neatseq_flow_modules.GATK_modules.GATK_CatVariants
    neatseq_flow_modules.GATK_modules.GATK_gvcf
    neatseq_flow_modules.GATK_modules.GATK_hard_filters
    neatseq_flow_modules.GATK_modules.GATK_merge_gvcf
    neatseq_flow_modules.GATK_modules.GATK_pre_processing
    neatseq_flow_modules.GATK_modules.GATK_SelectVariants
    neatseq_flow_modules.GATK_modules.GATK_VQSR
    neatseq_flow_modules.GATK_modules.GenotypeGVCFs
    neatseq_flow_modules.GATK_modules.Picard_CollectAlignmentSummaryMatrics
    neatseq_flow_modules.GATK_modules.Picard_CollectVariantCalling
    neatseq_flow_modules.GATK_modules.STAT_VEP
    neatseq_flow_modules.GATK_modules.VEP
    neatseq_flow_modules.Liron.cgMLST_and_MLST_typing_module.cgMLST_and_MLST_typing
    neatseq_flow_modules.Liron.Collect_results_module.Collect_results
    neatseq_flow_modules.Liron.Cutadapt_module.Cutadapt
    neatseq_flow_modules.Liron.DeSeq2_module.DeSeq2
    neatseq_flow_modules.Liron.Gassst_module.Gassst
    neatseq_flow_modules.Liron.Gubbins_module.Gubbins
    neatseq_flow_modules.Liron.Prokka_module.Prokka
    neatseq_flow_modules.Liron.Roary_module.Roary
    neatseq_flow_modules.Liron.RSEM_module.RSEM
    neatseq_flow_modules.Liron.Snippy_module.Snippy
    neatseq_flow_modules.Liron.Tree_plot_module.Tree_plot
    neatseq_flow_modules.Liron.Trim_Galore_module.Trim_Galore
    neatseq_flow_modules.main_NSF_classes.Assembly.quast
    neatseq_flow_modules.main_NSF_classes.Assembly.spades_assembl
    neatseq_flow_modules.main_NSF_classes.ChIP_seq.macs2_callpeak
    neatseq_flow_modules.main_NSF_classes.Generic_module.Generic
    neatseq_flow_modules.main_NSF_classes.IGVtools.IGV_count
    neatseq_flow_modules.main_NSF_classes.IGVtools.IGV_toTDF
    neatseq_flow_modules.main_NSF_classes.mapping.bowtie1_builder
    neatseq_flow_modules.main_NSF_classes.mapping.bowtie1_mapper
    neatseq_flow_modules.main_NSF_classes.mapping.bowtie2_builder
    neatseq_flow_modules.main_NSF_classes.mapping.bowtie2_mapper
    neatseq_flow_modules.main_NSF_classes.mapping.bwa_builder
    neatseq_flow_modules.main_NSF_classes.mapping.bwa_mapper
    neatseq_flow_modules.main_NSF_classes.mapping.genomeCoverageBed
    neatseq_flow_modules.main_NSF_classes.mapping.samtools
    neatseq_flow_modules.main_NSF_classes.miscellaneous.Fillout_Generic
    neatseq_flow_modules.main_NSF_classes.miscellaneous.manage_types
    neatseq_flow_modules.main_NSF_classes.miscellaneous.merge_table
    neatseq_flow_modules.main_NSF_classes.miscellaneous.ProjectToSample
    neatseq_flow_modules.main_NSF_classes.miscellaneous.split_fasta
    neatseq_flow_modules.main_NSF_classes.preparing.fastqc_html
    neatseq_flow_modules.main_NSF_classes.preparing.Import
    neatseq_flow_modules.main_NSF_classes.preparing.trimmo
    neatseq_flow_modules.main_NSF_classes.Reports.Multiqc
    neatseq_flow_modules.main_NSF_classes.RNA_seq.add_trinity_tags
    neatseq_flow_modules.main_NSF_classes.RNA_seq.trinity
    neatseq_flow_modules.main_NSF_classes.searching.blast
    neatseq_flow_modules.main_NSF_classes.searching.makeblastdb
    neatseq_flow_modules.main_NSF_classes.UCSCtools.UCSC_BW_wig
    neatseq_flow_modules.main_NSF_classes.variants.vcftools
    neatseq_flow_modules.mapping.htseq_count
    neatseq_flow_modules.mapping.RSEM_mapper
    neatseq_flow_modules.mapping.RSEM_prep
    neatseq_flow_modules.mapping.STAR_builder
    neatseq_flow_modules.mapping.STAR_LoadRemoveGenome
    neatseq_flow_modules.mapping.STAR_mapper
    neatseq_flow_modules.mash_module.mash_dist
    neatseq_flow_modules.mash_module.mash_sketch
    neatseq_flow_modules.metagenomics.centrifuge
    neatseq_flow_modules.metagenomics.HUMAnN2
    neatseq_flow_modules.metagenomics.kaiju
    neatseq_flow_modules.metagenomics.kraken
    neatseq_flow_modules.metagenomics.kraken_biom
    neatseq_flow_modules.metagenomics.metaphlan2
    neatseq_flow_modules.microbiology.CARD_RGI
    neatseq_flow_modules.miscellaneous.fasta_splitter.fasta_splitter
    neatseq_flow_modules.QIIME.qiime_align_seqs
    neatseq_flow_modules.QIIME.qiime_assign_taxonomy
    neatseq_flow_modules.QIIME.qiime_chimera
    neatseq_flow_modules.QIIME.qiime_demult
    neatseq_flow_modules.QIIME.qiime_divers
    neatseq_flow_modules.QIIME.qiime_filter_alignment
    neatseq_flow_modules.QIIME.qiime_filter_otus
    neatseq_flow_modules.QIIME.qiime_filter_samples_from_otu_table
    neatseq_flow_modules.QIIME.qiime_make_otu_table
    neatseq_flow_modules.QIIME.qiime_make_phylogeny
    neatseq_flow_modules.QIIME.qiime_pick_otus
    neatseq_flow_modules.QIIME.qiime_pick_rep_set
    neatseq_flow_modules.QIIME.qiime_prep
    neatseq_flow_modules.QIIME.qiime_sort_otu_table
    neatseq_flow_modules.QIIME2.qiime2_general
    neatseq_flow_modules.QIIME2.qiime2_import
    neatseq_flow_modules.Reports.BUSCO
    neatseq_flow_modules.Reports.fastq_screen
    neatseq_flow_modules.Reports.NGSplot
    neatseq_flow_modules.RNA_seq.Trinity_gene_to_trans_map
    neatseq_flow_modules.RNA_seq.trinity_mapping
    neatseq_flow_modules.RNA_seq.trinity_statistics
    neatseq_flow_modules.RNA_seq.Trinotate_modules.TransDecoder
    neatseq_flow_modules.RNA_seq.Trinotate_modules.Trinotate
    neatseq_flow_modules.searching.hmmscan
    neatseq_flow_modules.searching.parse_blast
    neatseq_flow_modules.variants.freebayes
    neatseq_flow_modules.variants.mpileup_varscan