Workflows
Modules
Tutorials
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