Index

M

module neatseq_flow_modules.Annotation.prokka_old, [1] neatseq_flow_modules.Assembly.clc_assembl, [1] neatseq_flow_modules.Assembly.megahit_assembl, [1] neatseq_flow_modules.ChIP_seq.CEAS, [1] neatseq_flow_modules.ChIP_seq.macs2_bdgcmp, [1] neatseq_flow_modules.clustering.cd_hit, [1] neatseq_flow_modules.clustering.vsearch_cluster, [1] neatseq_flow_modules.clustering.vsearch_derepel, [1] neatseq_flow_modules.GATK_modules.CNV_per_Exon, [1] neatseq_flow_modules.GATK_modules.GATK_CatVariants, [1] neatseq_flow_modules.GATK_modules.GATK_gvcf, [1] neatseq_flow_modules.GATK_modules.GATK_hard_filters, [1] neatseq_flow_modules.GATK_modules.GATK_merge_gvcf, [1] neatseq_flow_modules.GATK_modules.GATK_pre_processing, [1] neatseq_flow_modules.GATK_modules.GATK_SelectVariants, [1] neatseq_flow_modules.GATK_modules.GATK_VQSR, [1] neatseq_flow_modules.GATK_modules.GenotypeGVCFs, [1] neatseq_flow_modules.GATK_modules.Picard_CollectAlignmentSummaryMatrics, [1] neatseq_flow_modules.GATK_modules.Picard_CollectVariantCalling, [1] neatseq_flow_modules.GATK_modules.STAT_VEP, [1] neatseq_flow_modules.GATK_modules.VEP, [1] neatseq_flow_modules.Liron.cgMLST_and_MLST_typing_module.cgMLST_and_MLST_typing, [1] neatseq_flow_modules.Liron.Collect_results_module.Collect_results, [1] neatseq_flow_modules.Liron.Cutadapt_module.Cutadapt, [1] neatseq_flow_modules.Liron.DeSeq2_module.DeSeq2, [1] neatseq_flow_modules.Liron.Gassst_module.Gassst, [1] neatseq_flow_modules.Liron.Gubbins_module.Gubbins, [1] neatseq_flow_modules.Liron.Prokka_module.Prokka, [1] neatseq_flow_modules.Liron.Roary_module.Roary, [1] neatseq_flow_modules.Liron.RSEM_module.RSEM, [1], [2], [3] neatseq_flow_modules.Liron.Snippy_module.Snippy, [1], [2], [3] neatseq_flow_modules.Liron.Tree_plot_module.Tree_plot, [1], [2], [3] neatseq_flow_modules.Liron.Trim_Galore_module.Trim_Galore, [1] neatseq_flow_modules.main_NSF_classes.Assembly.quast, [1], [2], [3] neatseq_flow_modules.main_NSF_classes.Assembly.spades_assembl, [1] neatseq_flow_modules.main_NSF_classes.ChIP_seq.macs2_callpeak, [1] neatseq_flow_modules.main_NSF_classes.Generic_module.Generic, [1] neatseq_flow_modules.main_NSF_classes.IGVtools.IGV_count, [1] neatseq_flow_modules.main_NSF_classes.IGVtools.IGV_toTDF, [1] neatseq_flow_modules.main_NSF_classes.mapping.bowtie1_builder, [1] neatseq_flow_modules.main_NSF_classes.mapping.bowtie1_mapper, [1] neatseq_flow_modules.main_NSF_classes.mapping.bowtie2_builder, [1] neatseq_flow_modules.main_NSF_classes.mapping.bowtie2_mapper, [1] neatseq_flow_modules.main_NSF_classes.mapping.bwa_builder, [1] neatseq_flow_modules.main_NSF_classes.mapping.bwa_mapper, [1] neatseq_flow_modules.main_NSF_classes.mapping.genomeCoverageBed, [1] neatseq_flow_modules.main_NSF_classes.mapping.samtools, [1] neatseq_flow_modules.main_NSF_classes.miscellaneous.Fillout_Generic, [1] neatseq_flow_modules.main_NSF_classes.miscellaneous.manage_types, [1] neatseq_flow_modules.main_NSF_classes.miscellaneous.merge_table, [1] neatseq_flow_modules.main_NSF_classes.miscellaneous.ProjectToSample, [1] neatseq_flow_modules.main_NSF_classes.miscellaneous.split_fasta, [1] neatseq_flow_modules.main_NSF_classes.preparing.fastqc_html, [1] neatseq_flow_modules.main_NSF_classes.preparing.Import, [1] neatseq_flow_modules.main_NSF_classes.preparing.trimmo, [1] neatseq_flow_modules.main_NSF_classes.Reports.Multiqc, [1], [2], [3], [4], [5] neatseq_flow_modules.main_NSF_classes.RNA_seq.add_trinity_tags, [1] neatseq_flow_modules.main_NSF_classes.RNA_seq.trinity, [1] neatseq_flow_modules.main_NSF_classes.searching.blast, [1] neatseq_flow_modules.main_NSF_classes.searching.makeblastdb, [1] neatseq_flow_modules.main_NSF_classes.UCSCtools.UCSC_BW_wig, [1] neatseq_flow_modules.main_NSF_classes.variants.vcftools, [1] neatseq_flow_modules.mapping.htseq_count, [1], [2], [3] neatseq_flow_modules.mapping.RSEM_mapper, [1] neatseq_flow_modules.mapping.RSEM_prep, [1] neatseq_flow_modules.mapping.STAR_builder, [1] neatseq_flow_modules.mapping.STAR_LoadRemoveGenome, [1] neatseq_flow_modules.mapping.STAR_mapper, [1] neatseq_flow_modules.mash_module.mash_dist, [1] neatseq_flow_modules.mash_module.mash_sketch, [1] neatseq_flow_modules.metagenomics.centrifuge, [1] neatseq_flow_modules.metagenomics.HUMAnN2, [1] neatseq_flow_modules.metagenomics.kaiju, [1] neatseq_flow_modules.metagenomics.kraken, [1] neatseq_flow_modules.metagenomics.kraken_biom, [1] neatseq_flow_modules.metagenomics.metaphlan2, [1] neatseq_flow_modules.microbiology.CARD_RGI, [1] neatseq_flow_modules.miscellaneous.fasta_splitter.fasta_splitter, [1] neatseq_flow_modules.QIIME.qiime_align_seqs, [1] neatseq_flow_modules.QIIME.qiime_assign_taxonomy, [1] neatseq_flow_modules.QIIME.qiime_chimera, [1] neatseq_flow_modules.QIIME.qiime_demult, [1] neatseq_flow_modules.QIIME.qiime_divers, [1] neatseq_flow_modules.QIIME.qiime_filter_alignment, [1] neatseq_flow_modules.QIIME.qiime_filter_otus, [1] neatseq_flow_modules.QIIME.qiime_filter_samples_from_otu_table, [1] neatseq_flow_modules.QIIME.qiime_make_otu_table, [1] neatseq_flow_modules.QIIME.qiime_make_phylogeny, [1] neatseq_flow_modules.QIIME.qiime_pick_otus, [1] neatseq_flow_modules.QIIME.qiime_pick_rep_set, [1] neatseq_flow_modules.QIIME.qiime_prep, [1] neatseq_flow_modules.QIIME.qiime_sort_otu_table, [1] neatseq_flow_modules.QIIME2.qiime2_general, [1] neatseq_flow_modules.QIIME2.qiime2_import, [1] neatseq_flow_modules.Reports.BUSCO, [1] neatseq_flow_modules.Reports.fastq_screen, [1] neatseq_flow_modules.Reports.NGSplot, [1] neatseq_flow_modules.RNA_seq.Trinity_gene_to_trans_map, [1] neatseq_flow_modules.RNA_seq.trinity_mapping, [1] neatseq_flow_modules.RNA_seq.trinity_statistics, [1] neatseq_flow_modules.RNA_seq.Trinotate_modules.TransDecoder, [1] neatseq_flow_modules.RNA_seq.Trinotate_modules.Trinotate, [1] neatseq_flow_modules.searching.hmmscan, [1] neatseq_flow_modules.searching.parse_blast, [1] neatseq_flow_modules.variants.freebayes, [1] neatseq_flow_modules.variants.mpileup_varscan, [1]

N

neatseq_flow_modules.Annotation.prokka_old module, [1] neatseq_flow_modules.Assembly.clc_assembl module, [1] neatseq_flow_modules.Assembly.megahit_assembl module, [1] neatseq_flow_modules.ChIP_seq.CEAS module, [1] neatseq_flow_modules.ChIP_seq.macs2_bdgcmp module, [1] neatseq_flow_modules.clustering.cd_hit module, [1] neatseq_flow_modules.clustering.vsearch_cluster module, [1] neatseq_flow_modules.clustering.vsearch_derepel module, [1] neatseq_flow_modules.GATK_modules.CNV_per_Exon module, [1] neatseq_flow_modules.GATK_modules.GATK_CatVariants module, [1] neatseq_flow_modules.GATK_modules.GATK_gvcf module, [1] neatseq_flow_modules.GATK_modules.GATK_hard_filters module, [1] neatseq_flow_modules.GATK_modules.GATK_merge_gvcf module, [1] neatseq_flow_modules.GATK_modules.GATK_pre_processing module, [1] neatseq_flow_modules.GATK_modules.GATK_SelectVariants module, [1] neatseq_flow_modules.GATK_modules.GATK_VQSR module, [1] neatseq_flow_modules.GATK_modules.GenotypeGVCFs module, [1] neatseq_flow_modules.GATK_modules.Picard_CollectAlignmentSummaryMatrics module, [1] neatseq_flow_modules.GATK_modules.Picard_CollectVariantCalling module, [1] neatseq_flow_modules.GATK_modules.STAT_VEP module, [1] neatseq_flow_modules.GATK_modules.VEP module, [1] neatseq_flow_modules.Liron.cgMLST_and_MLST_typing_module.cgMLST_and_MLST_typing module, [1] neatseq_flow_modules.Liron.Collect_results_module.Collect_results module, [1] neatseq_flow_modules.Liron.Cutadapt_module.Cutadapt module, [1] neatseq_flow_modules.Liron.DeSeq2_module.DeSeq2 module, [1] neatseq_flow_modules.Liron.Gassst_module.Gassst module, [1] neatseq_flow_modules.Liron.Gubbins_module.Gubbins module, [1] neatseq_flow_modules.Liron.Prokka_module.Prokka module, [1] neatseq_flow_modules.Liron.Roary_module.Roary module, [1] neatseq_flow_modules.Liron.RSEM_module.RSEM module, [1], [2], [3] neatseq_flow_modules.Liron.Snippy_module.Snippy module, [1], [2], [3] neatseq_flow_modules.Liron.Tree_plot_module.Tree_plot module, [1], [2], [3] neatseq_flow_modules.Liron.Trim_Galore_module.Trim_Galore module, [1] neatseq_flow_modules.main_NSF_classes.Assembly.quast module, [1], [2], [3] neatseq_flow_modules.main_NSF_classes.Assembly.spades_assembl module, [1] neatseq_flow_modules.main_NSF_classes.ChIP_seq.macs2_callpeak module, [1] neatseq_flow_modules.main_NSF_classes.Generic_module.Generic module, [1] neatseq_flow_modules.main_NSF_classes.IGVtools.IGV_count module, [1] neatseq_flow_modules.main_NSF_classes.IGVtools.IGV_toTDF module, [1] neatseq_flow_modules.main_NSF_classes.mapping.bowtie1_builder module, [1] neatseq_flow_modules.main_NSF_classes.mapping.bowtie1_mapper module, [1] neatseq_flow_modules.main_NSF_classes.mapping.bowtie2_builder module, [1] neatseq_flow_modules.main_NSF_classes.mapping.bowtie2_mapper module, [1] neatseq_flow_modules.main_NSF_classes.mapping.bwa_builder module, [1] neatseq_flow_modules.main_NSF_classes.mapping.bwa_mapper module, [1] neatseq_flow_modules.main_NSF_classes.mapping.genomeCoverageBed module, [1] neatseq_flow_modules.main_NSF_classes.mapping.samtools module, [1] neatseq_flow_modules.main_NSF_classes.miscellaneous.Fillout_Generic module, [1] neatseq_flow_modules.main_NSF_classes.miscellaneous.manage_types module, [1] neatseq_flow_modules.main_NSF_classes.miscellaneous.merge_table module, [1] neatseq_flow_modules.main_NSF_classes.miscellaneous.ProjectToSample module, [1] neatseq_flow_modules.main_NSF_classes.miscellaneous.split_fasta module, [1] neatseq_flow_modules.main_NSF_classes.preparing.fastqc_html module, [1]

neatseq_flow_modules.main_NSF_classes.preparing.Import module, [1] neatseq_flow_modules.main_NSF_classes.preparing.trimmo module, [1] neatseq_flow_modules.main_NSF_classes.Reports.Multiqc module, [1], [2], [3], [4], [5] neatseq_flow_modules.main_NSF_classes.RNA_seq.add_trinity_tags module, [1] neatseq_flow_modules.main_NSF_classes.RNA_seq.trinity module, [1] neatseq_flow_modules.main_NSF_classes.searching.blast module, [1] neatseq_flow_modules.main_NSF_classes.searching.makeblastdb module, [1] neatseq_flow_modules.main_NSF_classes.UCSCtools.UCSC_BW_wig module, [1] neatseq_flow_modules.main_NSF_classes.variants.vcftools module, [1] neatseq_flow_modules.mapping.htseq_count module, [1], [2], [3] neatseq_flow_modules.mapping.RSEM_mapper module, [1] neatseq_flow_modules.mapping.RSEM_prep module, [1] neatseq_flow_modules.mapping.STAR_builder module, [1] neatseq_flow_modules.mapping.STAR_LoadRemoveGenome module, [1] neatseq_flow_modules.mapping.STAR_mapper module, [1] neatseq_flow_modules.mash_module.mash_dist module, [1] neatseq_flow_modules.mash_module.mash_sketch module, [1] neatseq_flow_modules.metagenomics.centrifuge module, [1] neatseq_flow_modules.metagenomics.HUMAnN2 module, [1] neatseq_flow_modules.metagenomics.kaiju module, [1] neatseq_flow_modules.metagenomics.kraken module, [1] neatseq_flow_modules.metagenomics.kraken_biom module, [1] neatseq_flow_modules.metagenomics.metaphlan2 module, [1] neatseq_flow_modules.microbiology.CARD_RGI module, [1] neatseq_flow_modules.miscellaneous.fasta_splitter.fasta_splitter module, [1] neatseq_flow_modules.QIIME.qiime_align_seqs module, [1] neatseq_flow_modules.QIIME.qiime_assign_taxonomy module, [1] neatseq_flow_modules.QIIME.qiime_chimera module, [1] neatseq_flow_modules.QIIME.qiime_demult module, [1] neatseq_flow_modules.QIIME.qiime_divers module, [1] neatseq_flow_modules.QIIME.qiime_filter_alignment module, [1] neatseq_flow_modules.QIIME.qiime_filter_otus module, [1] neatseq_flow_modules.QIIME.qiime_filter_samples_from_otu_table module, [1] neatseq_flow_modules.QIIME.qiime_make_otu_table module, [1] neatseq_flow_modules.QIIME.qiime_make_phylogeny module, [1] neatseq_flow_modules.QIIME.qiime_pick_otus module, [1] neatseq_flow_modules.QIIME.qiime_pick_rep_set module, [1] neatseq_flow_modules.QIIME.qiime_prep module, [1] neatseq_flow_modules.QIIME.qiime_sort_otu_table module, [1] neatseq_flow_modules.QIIME2.qiime2_general module, [1] neatseq_flow_modules.QIIME2.qiime2_import module, [1] neatseq_flow_modules.Reports.BUSCO module, [1] neatseq_flow_modules.Reports.fastq_screen module, [1] neatseq_flow_modules.Reports.NGSplot module, [1] neatseq_flow_modules.RNA_seq.Trinity_gene_to_trans_map module, [1] neatseq_flow_modules.RNA_seq.trinity_mapping module, [1] neatseq_flow_modules.RNA_seq.trinity_statistics module, [1] neatseq_flow_modules.RNA_seq.Trinotate_modules.TransDecoder module, [1] neatseq_flow_modules.RNA_seq.Trinotate_modules.Trinotate module, [1] neatseq_flow_modules.searching.hmmscan module, [1] neatseq_flow_modules.searching.parse_blast module, [1] neatseq_flow_modules.variants.freebayes module, [1] neatseq_flow_modules.variants.mpileup_varscan module, [1]