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.

  • mirna 6
  • gff 4
  • isomir 4
  • miRNA 3
  • qc 2
  • nacho 2
  • nanostring 2
  • mRNA 2
  • smrnaseq 2
  • RNA sequencing 2
  • mirdeep2 2
  • QC 1
  • cluster 1
  • mapper 1
  • microRNA 1
  • microrna 1
  • target prediction 1
  • bam 0
  • fasta 0
  • vcf 0
  • fastq 0
  • genomics 0
  • metagenomics 0
  • genome 0
  • index 0
  • reference 0
  • alignment 0
  • assembly 0
  • bed 0
  • gatk4 0
  • cram 0
  • sam 0
  • sort 0
  • structural variants 0
  • variant calling 0
  • annotation 0
  • database 0
  • align 0
  • merge 0
  • filter 0
  • bacteria 0
  • map 0
  • statistics 0
  • coverage 0
  • variants 0
  • quality control 0
  • classification 0
  • download 0
  • classify 0
  • gtf 0
  • nanopore 0
  • cnv 0
  • split 0
  • gfa 0
  • taxonomic profiling 0
  • k-mer 0
  • variant 0
  • MSA 0
  • contamination 0
  • somatic 0
  • pacbio 0
  • taxonomy 0
  • sentieon 0
  • convert 0
  • count 0
  • proteomics 0
  • binning 0
  • quality 0
  • conversion 0
  • single-cell 0
  • VCF 0
  • copy number 0
  • clustering 0
  • ancient DNA 0
  • bedtools 0
  • imputation 0
  • phylogeny 0
  • contigs 0
  • bisulfite 0
  • mags 0
  • reporting 0
  • graph 0
  • variation graph 0
  • sv 0
  • isoseq 0
  • build 0
  • bcftools 0
  • trimming 0
  • long reads 0
  • gvcf 0
  • kmer 0
  • cna 0
  • rnaseq 0
  • wgs 0
  • illumina 0
  • bqsr 0
  • protein 0
  • databases 0
  • compression 0
  • indexing 0
  • bisulphite 0
  • methylseq 0
  • picard 0
  • consensus 0
  • methylation 0
  • table 0
  • metrics 0
  • imaging 0
  • antimicrobial resistance 0
  • taxonomic classification 0
  • long-read 0
  • phage 0
  • 5mC 0
  • mapping 0
  • visualisation 0
  • stats 0
  • demultiplex 0
  • openms 0
  • tsv 0
  • sequences 0
  • serotype 0
  • protein sequence 0
  • amr 0
  • base quality score recalibration 0
  • haplotype 0
  • histogram 0
  • scWGBS 0
  • WGBS 0
  • pairs 0
  • DNA methylation 0
  • pangenome graph 0
  • markduplicates 0
  • bins 0
  • searching 0
  • depth 0
  • aDNA 0
  • structure 0
  • plot 0
  • neural network 0
  • matrix 0
  • expression 0
  • validation 0
  • checkm 0
  • LAST 0
  • metagenome 0
  • genotype 0
  • completeness 0
  • archaeogenomics 0
  • repeat 0
  • biscuit 0
  • mmseqs2 0
  • palaeogenomics 0
  • virus 0
  • damage 0
  • bcf 0
  • mappability 0
  • filtering 0
  • annotate 0
  • db 0
  • bisulfite sequencing 0
  • cooler 0
  • bwa 0
  • aligner 0
  • low-coverage 0
  • samtools 0
  • iCLIP 0
  • machine learning 0
  • transcript 0
  • msa 0
  • hmmsearch 0
  • segmentation 0
  • decompression 0
  • gff3 0
  • mkref 0
  • dedup 0
  • peaks 0
  • population genetics 0
  • phasing 0
  • mag 0
  • transcriptome 0
  • kraken2 0
  • glimpse 0
  • bismark 0
  • blast 0
  • example 0
  • evaluation 0
  • genotyping 0
  • sequence 0
  • umi 0
  • ncbi 0
  • spatial 0
  • germline 0
  • seqkit 0
  • ucsc 0
  • newick 0
  • gene 0
  • complexity 0
  • feature 0
  • json 0
  • demultiplexing 0
  • prediction 0
  • antimicrobial resistance genes 0
  • report 0
  • bedGraph 0
  • deduplication 0
  • vsearch 0
  • antimicrobial peptides 0
  • differential 0
  • prokaryote 0
  • low frequency variant calling 0
  • cnvkit 0
  • scRNA-seq 0
  • kmers 0
  • tumor-only 0
  • pangenome 0
  • mitochondria 0
  • splicing 0
  • gzip 0
  • plasmid 0
  • hmmer 0
  • snp 0
  • single 0
  • duplicates 0
  • NCBI 0
  • short-read 0
  • multiple sequence alignment 0
  • amps 0
  • visualization 0
  • de novo 0
  • merging 0
  • benchmark 0
  • adapters 0
  • kallisto 0
  • summary 0
  • fragment 0
  • single cell 0
  • svtk 0
  • mem 0
  • arg 0
  • 3-letter genome 0
  • ptr 0
  • call 0
  • gridss 0
  • coptr 0
  • detection 0
  • query 0
  • profiling 0
  • diversity 0
  • mutect2 0
  • idXML 0
  • view 0
  • antibiotic resistance 0
  • interval 0
  • indels 0
  • mpileup 0
  • counts 0
  • tabular 0
  • microbiome 0
  • extract 0
  • csv 0
  • sourmash 0
  • deamination 0
  • riboseq 0
  • MAF 0
  • isolates 0
  • de novo assembly 0
  • text 0
  • wxs 0
  • clipping 0
  • cut 0
  • genome assembler 0
  • CLIP 0
  • bedgraph 0
  • bcl2fastq 0
  • archaeogenetics 0
  • bin 0
  • SV 0
  • haplotypecaller 0
  • circrna 0
  • STR 0
  • structural 0
  • gsea 0
  • interval_list 0
  • genmod 0
  • hic 0
  • miscoding lesions 0
  • diamond 0
  • public datasets 0
  • fgbio 0
  • bigwig 0
  • compress 0
  • compare 0
  • peak-calling 0
  • profile 0
  • snps 0
  • palaeogenetics 0
  • enrichment 0
  • phylogenetic placement 0
  • ranking 0
  • ganon 0
  • read depth 0
  • deep learning 0
  • paf 0
  • cat 0
  • fastx 0
  • ngscheckmate 0
  • matching 0
  • malt 0
  • telomere 0
  • concatenate 0
  • redundancy 0
  • union 0
  • ATAC-seq 0
  • family 0
  • bgzip 0
  • add 0
  • sketch 0
  • retrotransposon 0
  • BGC 0
  • normalization 0
  • biosynthetic gene cluster 0
  • fungi 0
  • propr 0
  • logratio 0
  • copy number alteration calling 0
  • hybrid capture sequencing 0
  • targeted sequencing 0
  • DNA sequencing 0
  • chunk 0
  • sequencing 0
  • reads 0
  • microsatellite 0
  • FASTQ 0
  • microarray 0
  • happy 0
  • ont 0
  • umitools 0
  • HiFi 0
  • hmmcopy 0
  • xeniumranger 0
  • ancestry 0
  • ccs 0
  • abundance 0
  • pypgx 0
  • reference-free 0
  • DNA sequence 0
  • sample 0
  • containment 0
  • ampir 0
  • parsing 0
  • preprocessing 0
  • resistance 0
  • quantification 0
  • amplicon sequences 0
  • typing 0
  • windowmasker 0
  • uncompress 0
  • untar 0
  • unzip 0
  • vrhyme 0
  • entrez 0
  • fastk 0
  • zip 0
  • npz 0
  • bedpe 0
  • guide tree 0
  • RNA 0
  • repeat expansion 0
  • fcs-gx 0
  • fingerprint 0
  • PCA 0
  • ambient RNA removal 0
  • transcriptomics 0
  • rna_structure 0
  • genotype-based deconvoltion 0
  • variant_calling 0
  • popscle 0
  • transposons 0
  • bacterial 0
  • organelle 0
  • gatk4spark 0
  • mzml 0
  • somatic variants 0
  • mtDNA 0
  • long_read 0
  • subsample 0
  • minimap2 0
  • html 0
  • covid 0
  • pan-genome 0
  • pairsam 0
  • score 0
  • mlst 0
  • genome assembly 0
  • polishing 0
  • transcripts 0
  • small indels 0
  • panel 0
  • krona 0
  • lineage 0
  • pseudoalignment 0
  • krona chart 0
  • reports 0
  • ligate 0
  • notebook 0
  • amplicon sequencing 0
  • dna 0
  • cfDNA 0
  • HMM 0
  • chimeras 0
  • PacBio 0
  • pangolin 0
  • structural_variants 0
  • uLTRA 0
  • SNP 0
  • tabix 0
  • survivor 0
  • UMI 0
  • spaceranger 0
  • informative sites 0
  • kinship 0
  • identity 0
  • relatedness 0
  • lossless 0
  • observations 0
  • shapeit 0
  • benchmarking 0
  • replace 0
  • duplication 0
  • rsem 0
  • wastewater 0
  • indel 0
  • spark 0
  • prokka 0
  • plink2 0
  • dictionary 0
  • fam 0
  • bim 0
  • insert 0
  • scores 0
  • archiving 0
  • converter 0
  • roh 0
  • dump 0
  • prefetch 0
  • kraken 0
  • arriba 0
  • fusion 0
  • cut up 0
  • mcmicro 0
  • pileup 0
  • image_analysis 0
  • quality trimming 0
  • hi-c 0
  • CRISPR 0
  • gene expression 0
  • eukaryotes 0
  • remove 0
  • cellranger 0
  • cool 0
  • virulence 0
  • clean 0
  • bakta 0
  • combine 0
  • mkfastq 0
  • bamtools 0
  • nucleotide 0
  • chromosome 0
  • prokaryotes 0
  • DRAMP 0
  • comparisons 0
  • image 0
  • fai 0
  • microbes 0
  • neubi 0
  • chip-seq 0
  • host 0
  • png 0
  • C to T 0
  • das tool 0
  • das_tool 0
  • bwameth 0
  • deeparg 0
  • complement 0
  • ataqv 0
  • wig 0
  • amplify 0
  • macrel 0
  • highly_multiplexed_imaging 0
  • genomes 0
  • aln 0
  • RNA-seq 0
  • atac-seq 0
  • rna 0
  • angsd 0
  • bracken 0
  • adapter trimming 0
  • genome mining 0
  • intervals 0
  • checkv 0
  • genetics 0
  • metamaps 0
  • concat 0
  • mask 0
  • ichorcna 0
  • hlala_typing 0
  • hla_typing 0
  • vcflib 0
  • functional analysis 0
  • hidden Markov model 0
  • hlala 0
  • lift 0
  • vg 0
  • leviosam2 0
  • hla 0
  • mapcounter 0
  • read-group 0
  • gene set analysis 0
  • interactions 0
  • aggregate 0
  • RNA-Seq 0
  • genome bins 0
  • simulate 0
  • ChIP-seq 0
  • import 0
  • artic 0
  • adapter 0
  • single cells 0
  • demultiplexed reads 0
  • genomad 0
  • preseq 0
  • library 0
  • gem 0
  • allele 0
  • amptransformer 0
  • ampgram 0
  • regression 0
  • differential expression 0
  • taxids 0
  • taxon name 0
  • zlib 0
  • trancriptome 0
  • tama 0
  • gstama 0
  • immunoprofiling 0
  • concordance 0
  • gene set 0
  • ped 0
  • vdj 0
  • variation 0
  • phase 0
  • bfiles 0
  • variant pruning 0
  • tbi 0
  • norm 0
  • orf 0
  • tree 0
  • megan 0
  • orthology 0
  • parallelized 0
  • windows 0
  • checksum 0
  • removal 0
  • transcriptomic 0
  • mudskipper 0
  • mitochondrion 0
  • intersection 0
  • edit distance 0
  • minhash 0
  • authentication 0
  • mash 0
  • nextclade 0
  • distance 0
  • registration 0
  • image_processing 0
  • NRPS 0
  • GC content 0
  • xz 0
  • resolve_bioscience 0
  • multiallelic 0
  • small variants 0
  • nucleotides 0
  • rgfa 0
  • cnvnator 0
  • homoploymer 0
  • tnhaplotyper2 0
  • spatial_transcriptomics 0
  • comparison 0
  • proportionality 0
  • secondary metabolites 0
  • profiles 0
  • MSI 0
  • instability 0
  • msi 0
  • tumor 0
  • micro-satellite-scan 0
  • msisensor-pro 0
  • RiPP 0
  • archive 0
  • instrain 0
  • trim 0
  • khmer 0
  • bustools 0
  • awk 0
  • salmon 0
  • BAM 0
  • blastn 0
  • reheader 0
  • scatter 0
  • normalize 0
  • screen 0
  • antismash 0
  • GPU-accelerated 0
  • polyA_tail 0
  • refine 0
  • maximum likelihood 0
  • iphop 0
  • intersect 0
  • proteome 0
  • ancient dna 0
  • kma 0
  • graph layout 0
  • primer 0
  • COBS 0
  • k-mer index 0
  • bloom filter 0
  • HOPS 0
  • lofreq 0
  • serogroup 0
  • antibiotics 0
  • barcode 0
  • pharokka 0
  • SimpleAF 0
  • function 0
  • MaltExtract 0
  • retrotransposons 0
  • long terminal repeat 0
  • pair 0
  • interactive 0
  • krakenuniq 0
  • long terminal retrotransposon 0
  • krakentools 0
  • baf 0
  • reformatting 0
  • duplex 0
  • cvnkit 0
  • cleaning 0
  • sequence analysis 0
  • correction 0
  • long-read sequencing 0
  • frame-shift correction 0
  • signature 0
  • microbial 0
  • tab 0
  • trgt 0
  • scaffolding 0
  • varcal 0
  • realignment 0
  • Pharmacogenetics 0
  • gwas 0
  • graft 0
  • deconvolution 0
  • small genome 0
  • estimation 0
  • de novo assembler 0
  • rtgtools 0
  • corrupted 0
  • emboss 0
  • interval list 0
  • salmonella 0
  • settings 0
  • filtermutectcalls 0
  • junctions 0
  • metadata 0
  • bayesian 0
  • seqtk 0
  • short reads 0
  • UMIs 0
  • xenograft 0
  • unaligned 0
  • fetch 0
  • join 0
  • GEO 0
  • soft-clipped clusters 0
  • cancer genomics 0
  • anndata 0
  • snpsift 0
  • gene labels 0
  • fixmate 0
  • metagenomic 0
  • doublets 0
  • reads merging 0
  • screening 0
  • pharmacogenetics 0
  • FracMinHash sketch 0
  • fusions 0
  • repeat_expansions 0
  • expansionhunterdenovo 0
  • CNV 0
  • cnv calling 0
  • effect prediction 0
  • merge mate pairs 0
  • snpeff 0
  • bam2fq 0
  • calling 0
  • collate 0
  • dict 0
  • identifier 0
  • sra-tools 0
  • allele-specific 0
  • Duplication purging 0
  • dereplicate 0
  • taxon tables 0
  • fasterq-dump 0
  • sequenzautils 0
  • otu tables 0
  • recombination 0
  • standardisation 0
  • eCLIP 0
  • repeats 0
  • standardise 0
  • runs_of_homozygosity 0
  • transformation 0
  • ome-tif 0
  • standardization 0
  • taxonomic profile 0
  • polish 0
  • Read depth 0
  • shigella 0
  • joint genotyping 0
  • gatk 0
  • scaffold 0
  • contig 0
  • duplicate 0
  • regions 0
  • blastp 0
  • eido 0
  • rename 0
  • MCMICRO 0
  • eigenstrat 0
  • spatial_omics 0
  • heatmap 0
  • Streptococcus pneumoniae 0
  • random forest 0
  • evidence 0
  • metagenomes 0
  • structural-variant calling 0
  • svdb 0
  • parse 0
  • samplesheet 0
  • deseq2 0
  • switch 0
  • validate 0
  • panelofnormals 0
  • purge duplications 0
  • format 0
  • rna-seq 0
  • workflow 0
  • longread 0
  • dist 0
  • snakemake 0
  • rare variants 0
  • reverse complement 0
  • eigenvectors 0
  • hicPCA 0
  • de-novo 0
  • error 0
  • dbnsfp 0
  • sliding 0
  • POA 0
  • snippy 0
  • predictions 0
  • CRAM 0
  • autofluorescence 0
  • groupby 0
  • sliding window 0
  • tnscope 0
  • bgen 0
  • boxplot 0
  • dnascope 0
  • clr 0
  • alr 0
  • features 0
  • density 0
  • blat 0
  • chloroplast 0
  • SMN1 0
  • dnamodelapply 0
  • Read coverage histogram 0
  • confidence 0
  • core 0
  • workflow_mode 0
  • sha256 0
  • sniffles 0
  • createreadcountpanelofnormals 0
  • 256 bit 0
  • SMN2 0
  • boxcox 0
  • copyratios 0
  • propd 0
  • shinyngs 0
  • denoisereadcounts 0
  • readwriter 0
  • Escherichia coli 0
  • exploratory 0
  • cds 0
  • copy-number 0
  • readproteingroups 0
  • subsample bam 0
  • estimate 0
  • svtk/baftest 0
  • upd 0
  • uniparental 0
  • disomy 0
  • snv 0
  • sequencing_bias 0
  • downsample 0
  • downsample bam 0
  • short-read sequencing 0
  • countsvtypes 0
  • vcf2db 0
  • detecting svs 0
  • gemini 0
  • maf 0
  • lua 0
  • ATLAS 0
  • bias 0
  • variantcalling 0
  • sccmec 0
  • streptococcus 0
  • baftest 0
  • rdtest2vcf 0
  • spa 0
  • refflat 0
  • transcroder 0
  • sequencing adapters 0
  • atlas 0
  • bedgraphtobigwig 0
  • bigbed 0
  • bedtobigbed 0
  • eucaryotes 0
  • genepred 0
  • chromosomal rearrangements 0
  • gtftogenepred 0
  • rdtest 0
  • Mycobacterium tuberculosis 0
  • ucsc/liftover 0
  • mkarv 0
  • fast5 0
  • umicollapse 0
  • polya tail 0
  • post mortem damage 0
  • decompress 0
  • files 0
  • vcf2bed 0
  • toml 0
  • spatype 0
  • proteus 0
  • background 0
  • whamg 0
  • rRNA 0
  • wham 0
  • HLA 0
  • coding 0
  • ancientDNA 0
  • single-stranded 0
  • copy number analysis 0
  • gender determination 0
  • cycif 0
  • mashmap 0
  • copy number alterations 0
  • constant 0
  • copy number variation 0
  • yahs 0
  • geo 0
  • mapad 0
  • invariant 0
  • SNPs 0
  • adna 0
  • c to t 0
  • wavefront 0
  • all versus all 0
  • vcfbreakmulti 0
  • read group 0
  • uniq 0
  • deduplicate 0
  • VCFtools 0
  • verifybamid 0
  • DNA contamination estimation 0
  • construct 0
  • graph projection to vcf 0
  • http(s) 0
  • extractunbinned 0
  • fracminhash sketch 0
  • ribosomal RNA 0
  • hash sketch 0
  • linkbins 0
  • signatures 0
  • utility 0
  • sintax 0
  • vsearch/sort 0
  • authentict 0
  • usearch 0
  • long read alignment 0
  • pangenome-scale 0
  • scRNA-Seq 0
  • mgf 0
  • simulation 0
  • affy 0
  • tags 0
  • tag2tag 0
  • Staphylococcus aureus 0
  • hashing-based deconvolution 0
  • rank 0
  • java 0
  • script 0
  • xml 0
  • svg 0
  • standard 0
  • haplotag 0
  • staging 0
  • Staging 0
  • functional 0
  • multiqc 0
  • mass_error 0
  • search engine 0
  • poolseq 0
  • variant-calling 0
  • stardist 0
  • telseq 0
  • vsearch/dereplicate 0
  • vsearch/fastqfilter 0
  • fastqfilter 0
  • ATACseq 0
  • shift 0
  • ATACshift 0
  • setgt 0
  • impute-info 0
  • Illumina 0
  • translate 0
  • circular 0
  • bwamem2 0
  • bwameme 0
  • grabix 0
  • ribosomal 0
  • 10x 0
  • regulatory network 0
  • transcription factors 0
  • paraphase 0
  • selector 0
  • cram-size 0
  • size 0
  • quality check 0
  • realign 0
  • spot 0
  • uniques 0
  • orthogroup 0
  • orthologs 0
  • sage 0
  • mass spectrometry 0
  • featuretable 0
  • extraction 0
  • cgMLST 0
  • WGS 0
  • redundant 0
  • nanoq 0
  • Read filters 0
  • Read trimming 0
  • Read report 0
  • drug categorization 0
  • jvarkit 0
  • tar 0
  • Pacbio 0
  • run 0
  • scanpy 0
  • contiguate 0
  • plotting 0
  • regtools 0
  • leafcutter 0
  • split_kmers 0
  • recovery 0
  • mgi 0
  • sylph 0
  • identity-by-descent 0
  • decomposeblocksub 0
  • block substitutions 0
  • pdb 0
  • updatedata 0
  • human removal 0
  • chip 0
  • partitioning 0
  • malformed 0
  • fix 0
  • paired reads re-pairing 0
  • regex 0
  • patterns 0
  • doublet 0
  • Immune Deconvolution 0
  • Bioinformatics Tools 0
  • Computational Immunology 0
  • catpack 0
  • prepare 0
  • mzML 0
  • metagenome assembler 0
  • decontamination 0
  • tarball 0
  • doublet_detection 0
  • targz 0
  • bclconvert 0
  • nucBed 0
  • AT content 0
  • nucleotide content 0
  • elfasta 0
  • elprep 0
  • controlstatistics 0
  • source tracking 0
  • emoji 0
  • quality_control 0
  • reference panels 0
  • admixture 0
  • barcodes 0
  • hostile 0
  • subsetting 0
  • logFC 0
  • significance statistic 0
  • p-value 0
  • scvi 0
  • solo 0
  • import segmentation 0
  • nuclear segmentation 0
  • cell segmentation 0
  • adapterremoval 0
  • relabel 0
  • resegment 0
  • morphology 0
  • antimicrobial reistance 0
  • guidetree 0
  • AC/NS/AF 0
  • hmmfetch 0
  • AMPs 0
  • sequence similarity 0
  • spectral clustering 0
  • comparative genomics 0
  • deep variant 0
  • mutect 0
  • idx 0
  • transform 0
  • gaps 0
  • introns 0
  • install 0
  • joint-genotyping 0
  • genotypegvcf 0
  • model 0
  • parallel 0
  • co-orthology 0
  • plastid 0
  • resfinder 0
  • resistance genes 0
  • raw 0
  • parquet 0
  • parser 0
  • dbsnp 0
  • standardize 0
  • quarto 0
  • python 0
  • r 0
  • coexpression 0
  • correlation 0
  • corpcor 0
  • homology 0
  • immunoinformatics 0
  • phylogenetics 0
  • site frequency spectrum 0
  • decompose 0
  • transmembrane 0
  • genome graph 0
  • tnseq 0
  • decoy 0
  • htseq 0
  • rrna 0
  • installation 0
  • sompy 0
  • doCounts 0
  • purging 0
  • peak picking 0
  • allele counts 0
  • ancestral alleles 0
  • airrseq 0
  • derived alleles 0
  • tnfilter 0
  • nuclear contamination estimate 0
  • array_cgh 0
  • cytosure 0
  • post Post-processing 0
  • vector 0
  • gprofiler2 0
  • gost 0
  • rad 0
  • structural variant 0
  • bam2fastx 0
  • bam2fastq 0
  • immcantation 0
  • assay 0
  • minimum_evolution 0
  • vcflib/vcffixup 0
  • hamming-distance 0
  • mygene 0
  • go 0
  • pile up 0
  • nanopore sequencing 0
  • rna velocity 0
  • cobra 0
  • extension 0
  • grea 0
  • functional enrichment 0
  • translation 0
  • paired reads merging 0
  • overlap-based merging 0
  • check 0
  • hashing-based deconvoltion 0
  • tag 0
  • gnu 0
  • coreutils 0
  • generic 0
  • transposable element 0
  • retrieval 0
  • MMseqs2 0
  • InterProScan 0
  • busco 0
  • droplet based single cells 0
  • lexogen 0
  • genotype-based demultiplexing 0
  • donor deconvolution 0
  • cellsnp 0
  • trimfq 0
  • cell_barcodes 0
  • prior knowledge 0
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  • seqfu 0
  • nucleotide sequence 0
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  • predict 0
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  • mkvdjref 0
  • genome taxonomy database 0
  • archaea 0
  • gunc 0
  • gunzip 0
  • cellpose 0
  • gvcftools 0
  • extract_variants 0
  • genome summary 0
  • qa 0
  • abricate 0
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  • reblockgvcf 0
  • revert 0
  • selectvariants 0
  • shiftchain 0
  • shiftfasta 0
  • shiftintervals 0
  • site depth 0
  • splitcram 0
  • splitintervals 0
  • svannotate 0
  • svcluster 0
  • variantfiltration 0
  • recalibration model 0
  • gawk 0
  • quality assurnce 0
  • txt 0
  • file parsing 0
  • bgc 0
  • chromosome_visualization 0
  • genome profile 0
  • duplicate removal 0
  • compound 0
  • models 0
  • chromap 0
  • genome size 0
  • genome heterozygosity 0
  • repeat content 0
  • Salmonella Typhi 0
  • Mykrobe 0
  • extractvariants 0
  • amrfinderplus 0
  • printreads 0
  • subtyping 0
  • probability_maps 0
  • population genomics 0
  • interproscan 0
  • genomic islands 0
  • insertion 0
  • postprocessing 0
  • jasminesv 0
  • jasmine 0
  • Python 0
  • Jupyter 0
  • jupytext 0
  • papermill 0
  • tblastn 0
  • Salmonella enterica 0
  • pixel classification 0
  • kallisto/index 0
  • quant 0
  • sorted 0
  • digital normalization 0
  • k-mer counting 0
  • effective genome size 0
  • Klebsiella 0
  • pneumoniae 0
  • file manipulation 0
  • kegg 0
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  • combining 0
  • bioawk 0
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  • pixel_classification 0
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  • readcounter 0
  • rgi 0
  • ibd 0
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  • mitochondrial 0
  • haplogroups 0
  • hifi 0
  • Assembly 0
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  • haplotype resolution 0
  • domains 0
  • compartments 0
  • topology 0
  • gccounter 0
  • calder2 0
  • genome browser 0
  • reformat 0
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  • track 0
  • Hidden Markov Model 0
  • hmtnote 0
  • annotations 0
  • pos 0
  • haemophilus 0
  • panel_of_normals 0
  • IDR 0
  • igv 0
  • igv.js 0
  • js 0
  • printsvevidence 0
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  • reorder 0
  • ENA 0
  • TMA dearray 0
  • UNet 0
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  • genomic bins 0
  • makebins 0
  • str 0
  • faqcs 0
  • antibiotic resistance genes 0
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  • enzyme 0
  • digest 0
  • SRA 0
  • public 0
  • Cores 0
  • cload 0
  • cooler/balance 0
  • consensus sequence 0
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  • subcontigs 0
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  • single molecule 0
  • generate 0
  • random 0
  • Segmentation 0
  • cache 0
  • fq 0
  • PEP 0
  • corrrelation 0
  • scatterplot 0
  • cumulative coverage 0
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  • segment 0
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  • depth information 0
  • escherichia coli 0
  • schema 0
  • percent on target 0
  • pep 0
  • eigenstratdatabasetools 0
  • eklipse 0
  • na 0
  • circos 0
  • deletion 0
  • version 0
  • split by chromosome 0
  • custom 0
  • embl 0
  • genbank 0
  • swissprot 0
  • Streptococcus pyogenes 0
  • endogenous DNA 0
  • lint 0
  • partition histograms 0
  • postprocessgermlinecnvcalls 0
  • genomicsdbimport 0
  • condensedepthevidence 0
  • createsequencedictionary 0
  • polymorphic 0
  • createsomaticpanelofnormals 0
  • polymut 0
  • determinegermlinecontigploidy 0
  • duplication metrics 0
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  • filterintervals 0
  • filtervarianttranches 0
  • tranche filtering 0
  • gatherbqsrreports 0
  • genomicsdb 0
  • jointgenotyping 0
  • composestrtablefile 0
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  • germline contig ploidy 0
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  • splice 0
  • indexfeaturefile 0
  • learnreadorientationmodel 0
  • readorientationartifacts 0
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  • mergebamalignment 0
  • mutectstats 0
  • snvs 0
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  • short variant discovery 0
  • rust 0
  • targets 0
  • variant caller 0
  • somatic variant calling 0
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  • target 0
  • bootstrapping 0
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  • gamma 0
  • gene-calling 0
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  • export 0
  • antitarget 0
  • heattree 0
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  • insertions 0
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  • clumping fastqs 0
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miRanda is an algorithm for finding genomic targets for microRNAs

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txt versions

miRDeep2 Mapper is a tool that prepares deep sequencing reads for downstream miRNA detection by collapsing reads, mapping them to a genome, and outputting the required files for miRNA discovery.

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outputs versions

mirdeep2:

miRDeep2 Mapper (mapper.pl) is part of the miRDeep2 suite. It collapses identical reads, maps them to a reference genome, and outputs both collapsed FASTA and ARF files for downstream miRNA detection and analysis.

miRDeep2 is a tool for identifying known and novel miRNAs in deep sequencing data by analyzing sequenced RNAs. It integrates the mapping of sequencing reads to the genome and predicts miRNA precursors and mature miRNAs.

012010123

outputs versions

mirdeep2:

miRDeep2 is a tool that discovers microRNA genes by analyzing sequenced RNAs. It includes three main scripts: miRDeep2.pl, mapper.pl, and quantifier.pl for comprehensive miRNA detection and quantification.

mirtop counts generates a file with the minimal information about each sequence and the count data in columns for each samples.

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tsv versions

mirtop:

Small RNA-seq annotation

mirtop export generates files such as fasta, vcf or compatible with isomiRs bioconductor package

0101012

tsv fasta vcf versions

mirtop:

Small RNA-seq annotation

mirtop gff generates the GFF3 adapter format to capture miRNA variations

0101012

gff versions

mirtop:

Small RNA-seq annotation

mirtop gff gets the number of isomiRs and miRNAs annotated in the GFF file by isomiR category.

01

txt log versions

mirtop:

Small RNA-seq annotation

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.

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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.

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