Available Modules

Modules are the building stones of all DSL2 nf-core blocks. You can find more info from nf-core website, if you would like to write your own module.

  • spaceranger 3
  • index 2
  • reference 2
  • qc 2
  • mkref 2
  • miRNA 2
  • smrnaseq 2
  • mRNA 2
  • nacho 2
  • nanostring 2
  • align 1
  • count 1
  • rnaseq 1
  • QC 1
  • imaging 1
  • cluster 1
  • spatial 1
  • differential 1
  • mirna 1
  • riboseq 1
  • microRNA 1
  • translation 1
  • bam 0
  • fasta 0
  • vcf 0
  • fastq 0
  • genomics 0
  • metagenomics 0
  • genome 0
  • alignment 0
  • assembly 0
  • bed 0
  • gatk4 0
  • cram 0
  • sort 0
  • sam 0
  • structural variants 0
  • variant calling 0
  • annotation 0
  • database 0
  • merge 0
  • filter 0
  • gff 0
  • bacteria 0
  • map 0
  • statistics 0
  • coverage 0
  • variants 0
  • classification 0
  • classify 0
  • nanopore 0
  • quality control 0
  • download 0
  • gtf 0
  • cnv 0
  • split 0
  • MSA 0
  • k-mer 0
  • contamination 0
  • variant 0
  • taxonomy 0
  • taxonomic profiling 0
  • gfa 0
  • sentieon 0
  • somatic 0
  • pacbio 0
  • convert 0
  • conversion 0
  • clustering 0
  • proteomics 0
  • quality 0
  • binning 0
  • copy number 0
  • ancient DNA 0
  • single-cell 0
  • VCF 0
  • imputation 0
  • bedtools 0
  • trimming 0
  • phylogeny 0
  • contigs 0
  • mags 0
  • build 0
  • graph 0
  • long reads 0
  • kmer 0
  • isoseq 0
  • gvcf 0
  • sv 0
  • bcftools 0
  • bisulfite 0
  • variation graph 0
  • reporting 0
  • bqsr 0
  • illumina 0
  • table 0
  • long-read 0
  • picard 0
  • indexing 0
  • wgs 0
  • databases 0
  • cna 0
  • consensus 0
  • bisulphite 0
  • methylseq 0
  • protein 0
  • methylation 0
  • compression 0
  • stats 0
  • visualisation 0
  • serotype 0
  • phage 0
  • openms 0
  • metrics 0
  • tsv 0
  • demultiplex 0
  • 5mC 0
  • taxonomic classification 0
  • antimicrobial resistance 0
  • sequences 0
  • mapping 0
  • depth 0
  • bins 0
  • histogram 0
  • WGBS 0
  • scWGBS 0
  • pairs 0
  • searching 0
  • pangenome graph 0
  • structure 0
  • expression 0
  • aDNA 0
  • protein sequence 0
  • base quality score recalibration 0
  • amr 0
  • plot 0
  • markduplicates 0
  • haplotype 0
  • DNA methylation 0
  • neural network 0
  • matrix 0
  • palaeogenomics 0
  • archaeogenomics 0
  • repeat 0
  • mmseqs2 0
  • mappability 0
  • db 0
  • samtools 0
  • machine learning 0
  • iCLIP 0
  • checkm 0
  • genotype 0
  • annotate 0
  • bwa 0
  • damage 0
  • completeness 0
  • metagenome 0
  • filtering 0
  • virus 0
  • LAST 0
  • gzip 0
  • validation 0
  • transcript 0
  • biscuit 0
  • low-coverage 0
  • bcf 0
  • bisulfite sequencing 0
  • cooler 0
  • aligner 0
  • mag 0
  • blast 0
  • decompression 0
  • ncbi 0
  • newick 0
  • umi 0
  • glimpse 0
  • population genetics 0
  • bismark 0
  • gff3 0
  • hmmsearch 0
  • evaluation 0
  • gene 0
  • segmentation 0
  • peaks 0
  • msa 0
  • hmmer 0
  • seqkit 0
  • complexity 0
  • example 0
  • phasing 0
  • genotyping 0
  • ucsc 0
  • sequence 0
  • transcriptome 0
  • kraken2 0
  • dedup 0
  • germline 0
  • mitochondria 0
  • demultiplexing 0
  • prokaryote 0
  • snp 0
  • feature 0
  • deduplication 0
  • antimicrobial resistance genes 0
  • single 0
  • plasmid 0
  • antimicrobial peptides 0
  • pangenome 0
  • splicing 0
  • json 0
  • multiple sequence alignment 0
  • cnvkit 0
  • scRNA-seq 0
  • prediction 0
  • low frequency variant calling 0
  • kmers 0
  • tumor-only 0
  • NCBI 0
  • duplicates 0
  • short-read 0
  • report 0
  • vsearch 0
  • bedGraph 0
  • svtk 0
  • isolates 0
  • amps 0
  • de novo 0
  • diversity 0
  • tabular 0
  • single cell 0
  • text 0
  • sourmash 0
  • call 0
  • FASTQ 0
  • fragment 0
  • csv 0
  • cat 0
  • mem 0
  • concatenate 0
  • 3-letter genome 0
  • extract 0
  • ptr 0
  • indels 0
  • mutect2 0
  • microbiome 0
  • counts 0
  • query 0
  • view 0
  • clipping 0
  • coptr 0
  • deamination 0
  • mpileup 0
  • interval 0
  • visualization 0
  • summary 0
  • MAF 0
  • antibiotic resistance 0
  • benchmark 0
  • detection 0
  • idXML 0
  • de novo assembly 0
  • arg 0
  • gridss 0
  • wxs 0
  • adapters 0
  • profiling 0
  • structural 0
  • profile 0
  • merging 0
  • kallisto 0
  • preprocessing 0
  • containment 0
  • deep learning 0
  • interval_list 0
  • rna 0
  • peak-calling 0
  • compare 0
  • ranking 0
  • genmod 0
  • bedgraph 0
  • enrichment 0
  • happy 0
  • read depth 0
  • HiFi 0
  • CLIP 0
  • hmmcopy 0
  • haplotypecaller 0
  • biosynthetic gene cluster 0
  • ccs 0
  • HMM 0
  • fastx 0
  • microarray 0
  • sequencing 0
  • mtDNA 0
  • snps 0
  • copy number alteration calling 0
  • hybrid capture sequencing 0
  • targeted sequencing 0
  • DNA sequencing 0
  • diamond 0
  • SV 0
  • miscoding lesions 0
  • palaeogenetics 0
  • archaeogenetics 0
  • sample 0
  • bigwig 0
  • bin 0
  • gsea 0
  • family 0
  • bgzip 0
  • genome assembler 0
  • hic 0
  • ganon 0
  • quantification 0
  • reference-free 0
  • compress 0
  • paf 0
  • ancestry 0
  • public datasets 0
  • microsatellite 0
  • fgbio 0
  • reads 0
  • ngscheckmate 0
  • matching 0
  • STR 0
  • phylogenetic placement 0
  • BGC 0
  • cut 0
  • circrna 0
  • malt 0
  • ont 0
  • image 0
  • umitools 0
  • abundance 0
  • DNA sequence 0
  • ampir 0
  • logratio 0
  • propr 0
  • bedpe 0
  • redundancy 0
  • add 0
  • sketch 0
  • parsing 0
  • xeniumranger 0
  • telomere 0
  • normalization 0
  • retrotransposon 0
  • chunk 0
  • transcriptomics 0
  • ATAC-seq 0
  • resistance 0
  • isomir 0
  • fungi 0
  • pypgx 0
  • bcl2fastq 0
  • union 0
  • relatedness 0
  • hidden Markov model 0
  • quality trimming 0
  • atac-seq 0
  • fai 0
  • wig 0
  • bacterial 0
  • ataqv 0
  • somatic variants 0
  • transposons 0
  • chip-seq 0
  • rna_structure 0
  • intervals 0
  • RNA 0
  • converter 0
  • mzml 0
  • adapter trimming 0
  • highly_multiplexed_imaging 0
  • prokka 0
  • ambient RNA removal 0
  • panel 0
  • chromosome 0
  • fastk 0
  • genomes 0
  • duplication 0
  • mlst 0
  • PacBio 0
  • PCA 0
  • scores 0
  • uLTRA 0
  • rsem 0
  • survivor 0
  • popscle 0
  • gene expression 0
  • fingerprint 0
  • repeat expansion 0
  • UMI 0
  • comparisons 0
  • pseudoalignment 0
  • organelle 0
  • krona chart 0
  • entrez 0
  • complement 0
  • tabix 0
  • structural_variants 0
  • krona 0
  • typing 0
  • dictionary 0
  • remove 0
  • lineage 0
  • pangolin 0
  • covid 0
  • pan-genome 0
  • pairsam 0
  • replace 0
  • angsd 0
  • mcmicro 0
  • html 0
  • cfDNA 0
  • gatk4spark 0
  • image_analysis 0
  • dna 0
  • genotype-based deconvoltion 0
  • plink2 0
  • roh 0
  • insert 0
  • png 0
  • amplicon sequencing 0
  • notebook 0
  • fam 0
  • reports 0
  • bim 0
  • kraken 0
  • variant_calling 0
  • DRAMP 0
  • deeparg 0
  • cool 0
  • cut up 0
  • untar 0
  • hi-c 0
  • uncompress 0
  • unzip 0
  • zip 0
  • eukaryotes 0
  • shapeit 0
  • archiving 0
  • ligate 0
  • checkv 0
  • dump 0
  • amplify 0
  • polishing 0
  • benchmarking 0
  • macrel 0
  • score 0
  • distance 0
  • long_read 0
  • genome mining 0
  • genome assembly 0
  • identity 0
  • transcripts 0
  • host 0
  • bamtools 0
  • minimap2 0
  • lossless 0
  • prokaryotes 0
  • kinship 0
  • mkfastq 0
  • informative sites 0
  • observations 0
  • virulence 0
  • nucleotide 0
  • wastewater 0
  • clean 0
  • indel 0
  • C to T 0
  • bwameth 0
  • amplicon sequences 0
  • fusion 0
  • chimeras 0
  • sylph 0
  • windowmasker 0
  • npz 0
  • subsample 0
  • mapper 0
  • das tool 0
  • arriba 0
  • guide tree 0
  • das_tool 0
  • combine 0
  • spark 0
  • neubi 0
  • fcs-gx 0
  • prefetch 0
  • cellranger 0
  • RNA-seq 0
  • pileup 0
  • CRISPR 0
  • aln 0
  • small indels 0
  • SNP 0
  • bakta 0
  • microbes 0
  • vrhyme 0
  • bracken 0
  • krakenuniq 0
  • barcode 0
  • primer 0
  • metamaps 0
  • pair 0
  • regression 0
  • interactive 0
  • krakentools 0
  • lift 0
  • interactions 0
  • serogroup 0
  • functional analysis 0
  • genetics 0
  • lofreq 0
  • reformat 0
  • taxids 0
  • gene set 0
  • dereplicate 0
  • repeats 0
  • haplogroups 0
  • ome-tif 0
  • MCMICRO 0
  • trancriptome 0
  • tama 0
  • gstama 0
  • mirdeep2 0
  • RNA sequencing 0
  • hla 0
  • gene set analysis 0
  • frame-shift correction 0
  • pigz 0
  • phase 0
  • standardise 0
  • concordance 0
  • standardization 0
  • Pharmacogenetics 0
  • long-read sequencing 0
  • hlala 0
  • screen 0
  • refine 0
  • khmer 0
  • bustools 0
  • taxon name 0
  • zlib 0
  • differential expression 0
  • find 0
  • variation 0
  • polyA_tail 0
  • ampgram 0
  • maximum likelihood 0
  • hla_typing 0
  • iphop 0
  • instrain 0
  • ichorcna 0
  • amptransformer 0
  • minhash 0
  • mask 0
  • pharmacogenetics 0
  • mapcounter 0
  • sequence analysis 0
  • hlala_typing 0
  • leviosam2 0
  • graph layout 0
  • tree 0
  • proportionality 0
  • SimpleAF 0
  • scaffolding 0
  • image_processing 0
  • rtgtools 0
  • registration 0
  • junctions 0
  • mitochondrion 0
  • runs_of_homozygosity 0
  • polish 0
  • scaffold 0
  • comparison 0
  • collate 0
  • cnvnator 0
  • nucleotides 0
  • multiallelic 0
  • contig 0
  • small variants 0
  • rgfa 0
  • duplicate 0
  • Read depth 0
  • tnhaplotyper2 0
  • Duplication purging 0
  • purge duplications 0
  • bam2fq 0
  • dict 0
  • cleaning 0
  • sequenzautils 0
  • cancer genomics 0
  • split_kmers 0
  • snpsift 0
  • snpeff 0
  • effect prediction 0
  • FracMinHash sketch 0
  • shigella 0
  • trgt 0
  • switch 0
  • ancient dna 0
  • Streptococcus pneumoniae 0
  • transformation 0
  • fixmate 0
  • rename 0
  • vcflib 0
  • seqtk 0
  • salmonella 0
  • varcal 0
  • corrupted 0
  • vg 0
  • fusions 0
  • soft-clipped clusters 0
  • signature 0
  • reformatting 0
  • library 0
  • orf 0
  • anndata 0
  • pharokka 0
  • function 0
  • msisensor-pro 0
  • micro-satellite-scan 0
  • tumor 0
  • msi 0
  • instability 0
  • MSI 0
  • homoploymer 0
  • retrotransposons 0
  • long terminal repeat 0
  • long terminal retrotransposon 0
  • nextclade 0
  • kma 0
  • svdb 0
  • spatial_transcriptomics 0
  • resolve_bioscience 0
  • profiles 0
  • salmon 0
  • GC content 0
  • doublets 0
  • megan 0
  • checksum 0
  • removal 0
  • gene labels 0
  • preseq 0
  • taxon tables 0
  • adapter 0
  • import 0
  • small genome 0
  • orthology 0
  • parallelized 0
  • variant pruning 0
  • bfiles 0
  • transcriptomic 0
  • screening 0
  • mudskipper 0
  • read-group 0
  • standardisation 0
  • ped 0
  • xz 0
  • archive 0
  • COBS 0
  • k-mer index 0
  • bloom filter 0
  • GPU-accelerated 0
  • join 0
  • de novo assembler 0
  • otu tables 0
  • taxonomic profile 0
  • mash 0
  • ChIP-seq 0
  • awk 0
  • aggregate 0
  • evidence 0
  • demultiplexed reads 0
  • metagenomes 0
  • random forest 0
  • spatial_omics 0
  • regions 0
  • artic 0
  • interval list 0
  • heatmap 0
  • allele-specific 0
  • rna-seq 0
  • deseq2 0
  • blastp 0
  • panelofnormals 0
  • structural-variant calling 0
  • microbial 0
  • joint genotyping 0
  • NRPS 0
  • RiPP 0
  • proteome 0
  • version 0
  • gatk 0
  • settings 0
  • sra-tools 0
  • simulate 0
  • antibiotics 0
  • blastn 0
  • antismash 0
  • fasterq-dump 0
  • BAM 0
  • RNA-Seq 0
  • realignment 0
  • eido 0
  • secondary metabolites 0
  • concat 0
  • duplex 0
  • fetch 0
  • intersect 0
  • GEO 0
  • tbi 0
  • tab 0
  • metadata 0
  • norm 0
  • repeat_expansions 0
  • expansionhunterdenovo 0
  • metagenomic 0
  • microscopy 0
  • trim 0
  • identifier 0
  • normalize 0
  • UMIs 0
  • format 0
  • intersection 0
  • deconvolution 0
  • bayesian 0
  • samplesheet 0
  • validate 0
  • windows 0
  • eigenstrat 0
  • emboss 0
  • scatter 0
  • merge mate pairs 0
  • reads merging 0
  • short reads 0
  • xenograft 0
  • graft 0
  • reheader 0
  • unaligned 0
  • correction 0
  • filtermutectcalls 0
  • vdj 0
  • gwas 0
  • gem 0
  • CNV 0
  • MaltExtract 0
  • baf 0
  • HOPS 0
  • immunoprofiling 0
  • cnv calling 0
  • authentication 0
  • genomad 0
  • calling 0
  • allele 0
  • edit distance 0
  • parse 0
  • genome bins 0
  • estimation 0
  • eCLIP 0
  • cvnkit 0
  • single cells 0
  • recombination 0
  • Escherichia coli 0
  • sompy 0
  • genomecov 0
  • closest 0
  • peak picking 0
  • bamtobed 0
  • maskfasta 0
  • site frequency spectrum 0
  • rrna 0
  • ancestral alleles 0
  • quality assurnce 0
  • derived alleles 0
  • tnfilter 0
  • sorting 0
  • autozygosity 0
  • homozygosity 0
  • biallelic 0
  • getfasta 0
  • overlap 0
  • htseq 0
  • chunking 0
  • overlapped bed 0
  • simulation 0
  • hmmfetch 0
  • decompose 0
  • polya tail 0
  • fast5 0
  • multinterval 0
  • Read coverage histogram 0
  • qa 0
  • decompress 0
  • reverse complement 0
  • propd 0
  • array_cgh 0
  • transmembrane 0
  • vcf2bed 0
  • genome graph 0
  • tnseq 0
  • jaccard 0
  • decoy 0
  • shiftBed 0
  • topology 0
  • gprofiler2 0
  • rdtest 0
  • transform 0
  • variantcalling 0
  • deep variant 0
  • mutect 0
  • idx 0
  • sccmec 0
  • streptococcus 0
  • csi 0
  • spa 0
  • deduping 0
  • gaps 0
  • comparative genomics 0
  • introns 0
  • smaller fastqs 0
  • clumping fastqs 0
  • install 0
  • spatype 0
  • splice 0
  • joint-genotyping 0
  • genotypegvcf 0
  • background_correction 0
  • fracminhash sketch 0
  • BCF 0
  • spectral clustering 0
  • rdtest2vcf 0
  • rad 0
  • countsvtypes 0
  • cytosure 0
  • update header 0
  • vector 0
  • boxcox 0
  • baftest 0
  • gost 0
  • svtk/baftest 0
  • chromap 0
  • duplicate removal 0
  • short-read sequencing 0
  • sequence similarity 0
  • detecting svs 0
  • chromosome_visualization 0
  • structural variant 0
  • bam2fastx 0
  • bam2fastq 0
  • immcantation 0
  • airrseq 0
  • immunoinformatics 0
  • co-orthology 0
  • homology 0
  • region 0
  • crispr 0
  • sizes 0
  • vsearch/sort 0
  • umicollapse 0
  • postprocessing 0
  • cellpose 0
  • tblastn 0
  • extractunbinned 0
  • linkbins 0
  • mkvdjref 0
  • multiomics 0
  • ucsc/liftover 0
  • sintax 0
  • gtftogenepred 0
  • scRNA-Seq 0
  • usearch 0
  • refflat 0
  • long read alignment 0
  • pangenome-scale 0
  • all versus all 0
  • genepred 0
  • mashmap 0
  • bedtobigbed 0
  • wavefront 0
  • whamg 0
  • hifi 0
  • graph projection to vcf 0
  • bigbed 0
  • lua 0
  • upd 0
  • uniparental 0
  • disomy 0
  • snv 0
  • downsample 0
  • downsample bam 0
  • subsample bam 0
  • vcf2db 0
  • gemini 0
  • maf 0
  • compartments 0
  • construct 0
  • files 0
  • toml 0
  • cadd 0
  • vcfbreakmulti 0
  • uniq 0
  • deduplicate 0
  • domains 0
  • VCFtools 0
  • verifybamid 0
  • DNA contamination estimation 0
  • Assembly 0
  • wham 0
  • subtyping 0
  • clr 0
  • antibody capture 0
  • chromosomal rearrangements 0
  • bioawk 0
  • createreadcountpanelofnormals 0
  • copyratios 0
  • denoisereadcounts 0
  • readwriter 0
  • dnamodelapply 0
  • Mycobacterium tuberculosis 0
  • dnascope 0
  • antigen capture 0
  • unionBedGraphs 0
  • workflow_mode 0
  • subtract 0
  • slopBed 0
  • groupby 0
  • tnscope 0
  • bgen 0
  • bases 0
  • chloroplast 0
  • confidence 0
  • calder2 0
  • blat 0
  • alr 0
  • eucaryotes 0
  • workflow 0
  • bedgraphtobigwig 0
  • adna 0
  • copy-number 0
  • copy number analysis 0
  • gender determination 0
  • Salmonella enterica 0
  • copy number alterations 0
  • copy number variation 0
  • yahs 0
  • geo 0
  • sequencing adapters 0
  • mapad 0
  • transcroder 0
  • snakemake 0
  • c to t 0
  • element 0
  • sorted 0
  • cds 0
  • proteus 0
  • readproteingroups 0
  • eigenvectors 0
  • hicPCA 0
  • sliding 0
  • file manipulation 0
  • coding 0
  • illumiation_correction 0
  • assay 0
  • trimBam 0
  • tar 0
  • variant-calling 0
  • stardist 0
  • telseq 0
  • vsearch/dereplicate 0
  • vsearch/fastqfilter 0
  • fastqfilter 0
  • ATACseq 0
  • shift 0
  • ATACshift 0
  • setgt 0
  • jvarkit 0
  • translate 0
  • tarball 0
  • search engine 0
  • targz 0
  • installation 0
  • doCounts 0
  • bclconvert 0
  • nucBed 0
  • AT content 0
  • nucleotide content 0
  • elfasta 0
  • elprep 0
  • allele counts 0
  • controlstatistics 0
  • source tracking 0
  • emoji 0
  • poolseq 0
  • mass_error 0
  • nuclear contamination estimate 0
  • tag2tag 0
  • cgMLST 0
  • WGS 0
  • redundant 0
  • nanoq 0
  • Read filters 0
  • Read trimming 0
  • Read report 0
  • drug categorization 0
  • uniques 0
  • Illumina 0
  • functional 0
  • impute-info 0
  • tags 0
  • hashing-based deconvolution 0
  • multiqc 0
  • rank 0
  • java 0
  • script 0
  • xml 0
  • svg 0
  • standard 0
  • haplotag 0
  • staging 0
  • Staging 0
  • http(s) 0
  • utility 0
  • HLA 0
  • quality_control 0
  • post Post-processing 0
  • featuretable 0
  • patterns 0
  • identity-by-descent 0
  • decomposeblocksub 0
  • block substitutions 0
  • pdb 0
  • run 0
  • updatedata 0
  • chip 0
  • partitioning 0
  • malformed 0
  • fix 0
  • paired reads re-pairing 0
  • regex 0
  • doublet 0
  • admixture 0
  • Immune Deconvolution 0
  • Bioinformatics Tools 0
  • Computational Immunology 0
  • catpack 0
  • prepare 0
  • mzML 0
  • taxonomic composition 0
  • antimicrobial reistance 0
  • contiguate 0
  • CRISPRi 0
  • 16S 0
  • hhsuite 0
  • hmmpress 0
  • adapterremoval 0
  • reference panels 0
  • doublet_detection 0
  • model 0
  • barcodes 0
  • subsetting 0
  • logFC 0
  • significance statistic 0
  • p-value 0
  • scvi 0
  • solo 0
  • import segmentation 0
  • nuclear segmentation 0
  • cell segmentation 0
  • relabel 0
  • resegment 0
  • morphology 0
  • hostile 0
  • mgi 0
  • decontamination 0
  • human removal 0
  • metagenome assembler 0
  • AMPs 0
  • antimicrobial peptide prediction 0
  • scanpy 0
  • amp 0
  • plotting 0
  • regtools 0
  • leafcutter 0
  • Staphylococcus aureus 0
  • affy 0
  • recovery 0
  • extraction 0
  • mass spectrometry 0
  • parallel 0
  • association 0
  • genotype likelihood 0
  • collapse 0
  • liftover 0
  • probabilistic realignment 0
  • seqfu 0
  • n50 0
  • cell_type_identification 0
  • cell_phenotyping 0
  • machine_learning 0
  • bacphlip 0
  • clahe 0
  • refresh 0
  • GWAS 0
  • hwe equilibrium 0
  • case/control 0
  • virulent 0
  • associations 0
  • spatial_neighborhoods 0
  • scimap 0
  • Bayesian 0
  • structural-variants 0
  • omics 0
  • biological activity 0
  • temperate 0
  • prior knowledge 0
  • tag 0
  • cell_barcodes 0
  • reference-independent 0
  • hwe statistics 0
  • go 0
  • r 0
  • bamUtil 0
  • plastid 0
  • resfinder 0
  • resistance genes 0
  • raw 0
  • mgf 0
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  • check 0
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  • generic 0
  • transposable element 0
  • retrieval 0
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  • sequencing_bias 0
  • MMseqs2 0
  • hash sketch 0
  • CRAM 0
  • polymut 0
  • NGS 0
  • qualities 0
  • AMP 0
  • peptide prediction 0
  • functional genomics 0
  • sgRNA 0
  • CRISPR-Cas9 0
  • maximum-likelihood 0
  • rra 0
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  • variant quality score recalibration 0
  • annotateintervals 0
  • DNA damage 0
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  • targets 0
  • estimate 0
  • taxonomic assignment 0
  • heattree 0
  • mash/sketch 0
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  • reduced 0
  • representations 0
  • maxbin2 0
  • gene-calling 0
  • metagenome-assembled genomes 0
  • gamma 0
  • lofreq/filter 0
  • asereadcounter 0
  • UShER 0
  • cnnscorevariants 0
  • Klebsiella 0
  • pneumoniae 0
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  • kegg 0
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  • combining 0
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  • collectreadcounts 0
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  • bedtointervallist 0
  • reorder 0
  • spliced 0
  • train 0
  • adapter removal 0
  • collapsing 0
  • getpileupsummaries 0
  • legionella 0
  • clinical 0
  • pneumophila 0
  • cross-samplecontamination 0
  • calculatecontamination 0
  • limma 0
  • Listeria monocytogenes 0
  • mass-spectroscopy 0
  • mcr-1 0
  • k-mer counting 0
  • consensus sequence 0
  • mitochondrial genome 0
  • reference genome 0
  • generate 0
  • single molecule 0
  • mosdepth 0
  • otu table 0
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  • groupreads 0
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  • scan 0
  • random 0
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  • bioinformatics tools 0
  • Beautiful stand-alone HTML report 0
  • GATK UnifiedGenotyper 0
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  • cancer genome 0
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  • MD5 0
  • 128 bit 0
  • megahit 0
  • denovo 0
  • debruijn 0
  • daa 0
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  • Neisseria meningitidis 0
  • bacterial variant calling 0
  • k-mer frequency 0
  • germline variant calling 0
  • 3D heat map 0
  • Merqury 0
  • lint 0
  • somatic variant calling 0
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  • ploidy 0
  • unionsum 0
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  • variant caller 0
  • methylation bias 0
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  • rust 0
  • fq 0
  • assembler 0
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  • svcluster 0
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  • gstama/polyacleanup 0
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  • splitcram 0
  • gunc 0
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  • site depth 0
  • gvcftools 0
  • extractvariants 0
  • variantfiltration 0
  • shiftintervals 0
  • abricate 0
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  • rgi 0
  • ibd 0
  • hbd 0
  • beagle 0
  • mitochondrial 0
  • shiftfasta 0
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  • Haemophilus influenzae 0
  • gstama/merge 0
  • TAMA 0
  • revert 0
  • genome profile 0
  • Mykrobe 0
  • genome summary 0
  • genome manipulation 0
  • genome statistics 0
  • Salmonella Typhi 0
  • repeat content 0
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  • gget 0
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  • Haplotypes 0
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  • variantrecalibrator 0
  • recalibration model 0
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  • digital normalization 0
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  • germline contig ploidy 0
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  • interproscan 0
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  • genomic islands 0
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  • genomicsdbimport 0
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  • Python 0
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  • tranche filtering 0
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Generally applicable transcriptome-wide analysis of translational efficiency using anota2seq

0123012

translated_mrna total_mrna translation buffering mrna_abundance rdata fold_change_plot interaction_p_distribution_plot residual_distribution_summary_plot residual_vs_fitted_plot rvm_fit_for_all_contrasts_group_plot rvm_fit_for_interactions_plot rvm_fit_for_omnibus_group_plot simulated_vs_obt_dfbetas_without_interaction_plot session_info versions

anota2seq:

Generally applicable transcriptome-wide analysis of translational efficiency using anota2seq

A tool for quality control and tracing taxonomic origins of microRNA sequencing data

0120

html json tsv all_fa rnatype_unknown_fa versions

mirtrace:

miRTrace is a new quality control and taxonomic tracing tool developed specifically for small RNA sequencing data (sRNA-Seq). Each sample is characterized by profiling sequencing quality, read length, sequencing depth and miRNA complexity and also the amounts of miRNAs versus undesirable sequences (derived from tRNAs, rRNAs and sequencing artifacts). In addition to these routine quality control (QC) analyses, miRTrace can accurately and sensitively resolve taxonomic origins of small RNA-Seq data based on the composition of clade-specific miRNAs. This feature can be used to detect cross-clade contaminations in typical lab settings. It can also be applied for more specific applications in forensics, food quality control and clinical diagnosis, for instance tracing the origins of meat products or detecting parasitic microRNAs in host serum.

NACHO (NAnostring quality Control dasHbOard) is developed for NanoString nCounter data. NanoString nCounter data is a messenger-RNA/micro-RNA (mRNA/miRNA) expression assay and works with fluorescent barcodes. Each barcode is assigned a mRNA/miRNA, which can be counted after bonding with its target. As a result each count of a specific barcode represents the presence of its target mRNA/miRNA.

0101

normalized_counts normalized_counts_wo_HK versions

NACHO:

R package that uses two main functions to summarize and visualize NanoString RCC files, namely: load_rcc() and visualise(). It also includes a function normalise(), which (re)calculates sample specific size factors and normalises the data. For more information vignette("NACHO") and vignette("NACHO-analysis")

NACHO (NAnostring quality Control dasHbOard) is developed for NanoString nCounter data. NanoString nCounter data is a messenger-RNA/micro-RNA (mRNA/miRNA) expression assay and works with fluorescent barcodes. Each barcode is assigned a mRNA/miRNA, which can be counted after bonding with its target. As a result each count of a specific barcode represents the presence of its target mRNA/miRNA.

0101

nacho_qc_reports nacho_qc_png nacho_qc_txt versions

NACHO:

R package that uses two main functions to summarize and visualize NanoString RCC files, namely: load_rcc() and visualise(). It also includes a function normalise(), which (re)calculates sample specific size factors and normalises the data. For more information vignette("NACHO") and vignette("NACHO-analysis")

Seqcluster collapse reduces computational complexity by collapsing identical sequences in a FASTQ file.

01

fastq versions

seqcluster:

Small RNA analysis from NGS data. Seqcluster generates a list of clusters of small RNA sequences, their genome location, their annotation and the abundance in all the sample of the project.

Module to use the 10x Space Ranger pipeline to process 10x spatial transcriptomics data

0123456700

outs versions

spaceranger:

Visium Spatial Gene Expression is a next-generation molecular profiling solution for classifying tissue based on total mRNA. Space Ranger is a set of analysis pipelines that process Visium Spatial Gene Expression data with brightfield and fluorescence microscope images. Space Ranger allows users to map the whole transcriptome in formalin fixed paraffin embedded (FFPE) and fresh frozen tissues to discover novel insights into normal development, disease pathology, and clinical translational research. Space Ranger provides pipelines for end to end analysis of Visium Spatial Gene Expression experiments.

Module to build a filtered GTF needed by the 10x Genomics Space Ranger tool. Uses the spaceranger mkgtf command.

0

gtf versions

spaceranger:

Visium Spatial Gene Expression is a next-generation molecular profiling solution for classifying tissue based on total mRNA. Space Ranger is a set of analysis pipelines that process Visium Spatial Gene Expression data with brightfield and fluorescence microscope images. Space Ranger allows users to map the whole transcriptome in formalin fixed paraffin embedded (FFPE) and fresh frozen tissues to discover novel insights into normal development, disease pathology, and clinical translational research. Space Ranger provides pipelines for end to end analysis of Visium Spatial Gene Expression experiments.

Module to build the reference needed by the 10x Genomics Space Ranger tool. Uses the spaceranger mkref command.

000

reference versions

spaceranger:

Visium Spatial Gene Expression is a next-generation molecular profiling solution for classifying tissue based on total mRNA. Space Ranger is a set of analysis pipelines that process Visium Spatial Gene Expression data with brightfield and fluorescence microscope images. Space Ranger allows users to map the whole transcriptome in formalin fixed paraffin embedded (FFPE) and fresh frozen tissues to discover novel insights into normal development, disease pathology, and clinical translational research. Space Ranger provides pipelines for end to end analysis of Visium Spatial Gene Expression experiments.

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