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.

  • bam 2
  • single-cell 2
  • doublets 2
  • fasta 1
  • fastq 1
  • genomics 1
  • variant calling 1
  • annotation 1
  • protein 1
  • antimicrobial resistance 1
  • transcript 1
  • gene 1
  • prediction 1
  • riboseq 1
  • dna 1
  • transcriptomics 1
  • cancer genomics 1
  • snpsift 1
  • evidence 1
  • predictions 1
  • dbnsfp 1
  • selector 1
  • doublet 1
  • doublet_detection 1
  • scvi 1
  • solo 1
  • predict 1
  • interproscan 1
  • vcf 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
  • database 0
  • align 0
  • merge 0
  • filter 0
  • gff 0
  • bacteria 0
  • map 0
  • statistics 0
  • coverage 0
  • qc 0
  • variants 0
  • quality control 0
  • classify 0
  • classification 0
  • gtf 0
  • download 0
  • cnv 0
  • nanopore 0
  • split 0
  • taxonomic profiling 0
  • variant 0
  • gfa 0
  • k-mer 0
  • MSA 0
  • contamination 0
  • pacbio 0
  • somatic 0
  • taxonomy 0
  • sentieon 0
  • convert 0
  • conversion 0
  • quality 0
  • binning 0
  • proteomics 0
  • count 0
  • clustering 0
  • VCF 0
  • ancient DNA 0
  • copy number 0
  • phylogeny 0
  • contigs 0
  • bedtools 0
  • imputation 0
  • bcftools 0
  • bisulfite 0
  • graph 0
  • isoseq 0
  • long reads 0
  • mags 0
  • gvcf 0
  • trimming 0
  • sv 0
  • variation graph 0
  • build 0
  • reporting 0
  • illumina 0
  • compression 0
  • picard 0
  • cna 0
  • bqsr 0
  • methylseq 0
  • kmer 0
  • rnaseq 0
  • consensus 0
  • indexing 0
  • QC 0
  • databases 0
  • wgs 0
  • table 0
  • bisulphite 0
  • methylation 0
  • stats 0
  • 5mC 0
  • long-read 0
  • phage 0
  • sequences 0
  • metrics 0
  • demultiplex 0
  • taxonomic classification 0
  • serotype 0
  • imaging 0
  • openms 0
  • tsv 0
  • visualisation 0
  • mapping 0
  • searching 0
  • matrix 0
  • histogram 0
  • structure 0
  • neural network 0
  • markduplicates 0
  • DNA methylation 0
  • plot 0
  • depth 0
  • amr 0
  • scWGBS 0
  • expression 0
  • WGBS 0
  • cluster 0
  • base quality score recalibration 0
  • bins 0
  • pangenome graph 0
  • protein sequence 0
  • aDNA 0
  • haplotype 0
  • pairs 0
  • damage 0
  • filtering 0
  • archaeogenomics 0
  • machine learning 0
  • bcf 0
  • palaeogenomics 0
  • mmseqs2 0
  • samtools 0
  • virus 0
  • low-coverage 0
  • validation 0
  • bisulfite sequencing 0
  • biscuit 0
  • bwa 0
  • iCLIP 0
  • completeness 0
  • metagenome 0
  • checkm 0
  • db 0
  • cooler 0
  • gzip 0
  • repeat 0
  • annotate 0
  • mappability 0
  • aligner 0
  • LAST 0
  • genotype 0
  • umi 0
  • mkref 0
  • hmmsearch 0
  • mag 0
  • bismark 0
  • gff3 0
  • dedup 0
  • population genetics 0
  • genotyping 0
  • germline 0
  • example 0
  • blast 0
  • segmentation 0
  • ncbi 0
  • ucsc 0
  • kraken2 0
  • transcriptome 0
  • phasing 0
  • sequence 0
  • newick 0
  • seqkit 0
  • peaks 0
  • glimpse 0
  • spatial 0
  • complexity 0
  • decompression 0
  • msa 0
  • evaluation 0
  • antimicrobial peptides 0
  • NCBI 0
  • vsearch 0
  • mitochondria 0
  • low frequency variant calling 0
  • single 0
  • short-read 0
  • feature 0
  • tumor-only 0
  • bedGraph 0
  • differential 0
  • scRNA-seq 0
  • duplicates 0
  • deduplication 0
  • demultiplexing 0
  • kmers 0
  • splicing 0
  • antimicrobial resistance genes 0
  • hmmer 0
  • report 0
  • prokaryote 0
  • snp 0
  • pangenome 0
  • cnvkit 0
  • json 0
  • mirna 0
  • plasmid 0
  • multiple sequence alignment 0
  • 3-letter genome 0
  • kallisto 0
  • concatenate 0
  • tabular 0
  • amps 0
  • single cell 0
  • mutect2 0
  • counts 0
  • cat 0
  • benchmark 0
  • idXML 0
  • antibiotic resistance 0
  • interval 0
  • gridss 0
  • text 0
  • arg 0
  • deamination 0
  • indels 0
  • de novo 0
  • visualization 0
  • MAF 0
  • csv 0
  • summary 0
  • view 0
  • query 0
  • mem 0
  • wxs 0
  • mpileup 0
  • extract 0
  • ptr 0
  • sourmash 0
  • coptr 0
  • detection 0
  • diversity 0
  • merging 0
  • isolates 0
  • call 0
  • profiling 0
  • de novo assembly 0
  • clipping 0
  • adapters 0
  • svtk 0
  • microbiome 0
  • fragment 0
  • pypgx 0
  • read depth 0
  • compress 0
  • gsea 0
  • cut 0
  • CLIP 0
  • quantification 0
  • isomir 0
  • ngscheckmate 0
  • paf 0
  • matching 0
  • retrotransposon 0
  • reads 0
  • microsatellite 0
  • hic 0
  • xeniumranger 0
  • reference-free 0
  • ccs 0
  • telomere 0
  • FASTQ 0
  • umitools 0
  • phylogenetic placement 0
  • ont 0
  • STR 0
  • DNA sequencing 0
  • enrichment 0
  • fgbio 0
  • sequencing 0
  • sample 0
  • genome assembler 0
  • hybrid capture sequencing 0
  • compare 0
  • ganon 0
  • peak-calling 0
  • ranking 0
  • interval_list 0
  • haplotypecaller 0
  • bgzip 0
  • genmod 0
  • fastx 0
  • targeted sequencing 0
  • public datasets 0
  • miscoding lesions 0
  • HiFi 0
  • palaeogenetics 0
  • preprocessing 0
  • archaeogenetics 0
  • redundancy 0
  • deep learning 0
  • family 0
  • propr 0
  • bedgraph 0
  • hmmcopy 0
  • happy 0
  • SV 0
  • bin 0
  • bigwig 0
  • profile 0
  • structural 0
  • diamond 0
  • copy number alteration calling 0
  • logratio 0
  • snps 0
  • mtDNA 0
  • circrna 0
  • containment 0
  • microarray 0
  • ampir 0
  • DNA sequence 0
  • abundance 0
  • ancestry 0
  • BGC 0
  • resistance 0
  • biosynthetic gene cluster 0
  • parsing 0
  • bcl2fastq 0
  • malt 0
  • normalization 0
  • ATAC-seq 0
  • sketch 0
  • add 0
  • chunk 0
  • fungi 0
  • union 0
  • host 0
  • identity 0
  • clean 0
  • kinship 0
  • typing 0
  • informative sites 0
  • amplicon sequences 0
  • entrez 0
  • fai 0
  • rsem 0
  • duplication 0
  • PacBio 0
  • DRAMP 0
  • bamtools 0
  • vrhyme 0
  • complement 0
  • fastk 0
  • miRNA 0
  • pileup 0
  • chimeras 0
  • atac-seq 0
  • relatedness 0
  • spaceranger 0
  • notebook 0
  • fingerprint 0
  • PCA 0
  • windowmasker 0
  • combine 0
  • comparisons 0
  • amplicon sequencing 0
  • bacterial 0
  • chromosome 0
  • variant_calling 0
  • HMM 0
  • virulence 0
  • arriba 0
  • benchmarking 0
  • fusion 0
  • fam 0
  • cfDNA 0
  • bim 0
  • transposons 0
  • bakta 0
  • pairsam 0
  • intervals 0
  • eukaryotes 0
  • spark 0
  • roh 0
  • zip 0
  • unzip 0
  • indel 0
  • uncompress 0
  • long_read 0
  • replace 0
  • RNA-seq 0
  • score 0
  • prokaryotes 0
  • quality trimming 0
  • prokka 0
  • insert 0
  • untar 0
  • RNA 0
  • remove 0
  • rna_structure 0
  • popscle 0
  • genotype-based deconvoltion 0
  • dictionary 0
  • genome assembly 0
  • pan-genome 0
  • ambient RNA removal 0
  • covid 0
  • converter 0
  • pangolin 0
  • UMI 0
  • lineage 0
  • plink2 0
  • krona chart 0
  • genome mining 0
  • structural_variants 0
  • ligate 0
  • archiving 0
  • uLTRA 0
  • subsample 0
  • SNP 0
  • minimap2 0
  • adapter trimming 0
  • tabix 0
  • survivor 0
  • transcripts 0
  • wastewater 0
  • reports 0
  • amplify 0
  • npz 0
  • mlst 0
  • ataqv 0
  • kraken 0
  • microbes 0
  • prefetch 0
  • mapper 0
  • fcs-gx 0
  • image 0
  • gatk4spark 0
  • observations 0
  • image_analysis 0
  • html 0
  • bwameth 0
  • C to T 0
  • aln 0
  • bedpe 0
  • hi-c 0
  • polishing 0
  • panel 0
  • mkfastq 0
  • nucleotide 0
  • somatic variants 0
  • cut up 0
  • dump 0
  • macrel 0
  • mzml 0
  • CRISPR 0
  • shapeit 0
  • cellranger 0
  • angsd 0
  • repeat expansion 0
  • gene expression 0
  • small indels 0
  • mcmicro 0
  • cool 0
  • das tool 0
  • lossless 0
  • rna 0
  • checkv 0
  • png 0
  • wig 0
  • organelle 0
  • genomes 0
  • chip-seq 0
  • deeparg 0
  • neubi 0
  • highly_multiplexed_imaging 0
  • bracken 0
  • scores 0
  • guide tree 0
  • das_tool 0
  • krona 0
  • pseudoalignment 0
  • concordance 0
  • ChIP-seq 0
  • leviosam2 0
  • lift 0
  • concat 0
  • genetics 0
  • homoploymer 0
  • registration 0
  • profiles 0
  • pigz 0
  • tnhaplotyper2 0
  • metamaps 0
  • SimpleAF 0
  • aggregate 0
  • tbi 0
  • ped 0
  • intersect 0
  • ampgram 0
  • distance 0
  • variation 0
  • resolve_bioscience 0
  • regression 0
  • interactions 0
  • taxon name 0
  • checksum 0
  • proportionality 0
  • comparison 0
  • cnvnator 0
  • megan 0
  • gem 0
  • tree 0
  • zlib 0
  • spatial_transcriptomics 0
  • minhash 0
  • demultiplexed reads 0
  • functional analysis 0
  • mitochondrion 0
  • GC content 0
  • baf 0
  • mash 0
  • genomad 0
  • multiallelic 0
  • read-group 0
  • small variants 0
  • taxids 0
  • rgfa 0
  • differential expression 0
  • nucleotides 0
  • tama 0
  • phase 0
  • krakentools 0
  • interactive 0
  • krakenuniq 0
  • mask 0
  • kma 0
  • long terminal retrotransposon 0
  • hidden Markov model 0
  • graph layout 0
  • long terminal repeat 0
  • retrotransposons 0
  • ichorcna 0
  • function 0
  • pharokka 0
  • transcriptomic 0
  • RNA-Seq 0
  • instrain 0
  • pair 0
  • polyA_tail 0
  • nextclade 0
  • bustools 0
  • xz 0
  • archive 0
  • khmer 0
  • screen 0
  • refine 0
  • bloom filter 0
  • COBS 0
  • maximum likelihood 0
  • iphop 0
  • k-mer index 0
  • simulate 0
  • mudskipper 0
  • mapcounter 0
  • xenograft 0
  • artic 0
  • MSI 0
  • msi 0
  • lofreq 0
  • instability 0
  • trancriptome 0
  • removal 0
  • orf 0
  • gstama 0
  • gwas 0
  • GPU-accelerated 0
  • reformatting 0
  • trim 0
  • vcflib 0
  • gene set 0
  • gene set analysis 0
  • serogroup 0
  • tumor 0
  • hlala_typing 0
  • micro-satellite-scan 0
  • hla_typing 0
  • hlala 0
  • hla 0
  • allele 0
  • msisensor-pro 0
  • graft 0
  • parallelized 0
  • barcode 0
  • orthology 0
  • haplogroups 0
  • salmon 0
  • vg 0
  • primer 0
  • amptransformer 0
  • variant pruning 0
  • antismash 0
  • effect prediction 0
  • validate 0
  • samplesheet 0
  • format 0
  • eido 0
  • scaffolding 0
  • pharmacogenetics 0
  • snpeff 0
  • blastp 0
  • eigenstrat 0
  • deseq2 0
  • rna-seq 0
  • awk 0
  • anndata 0
  • heatmap 0
  • regions 0
  • bam2fq 0
  • spatial_omics 0
  • join 0
  • rtgtools 0
  • BAM 0
  • MaltExtract 0
  • mirdeep2 0
  • RNA sequencing 0
  • metagenomic 0
  • identifier 0
  • smrnaseq 0
  • runs_of_homozygosity 0
  • signature 0
  • expansionhunterdenovo 0
  • repeat_expansions 0
  • intersection 0
  • sequence analysis 0
  • windows 0
  • metadata 0
  • FracMinHash sketch 0
  • tab 0
  • junctions 0
  • Pharmacogenetics 0
  • emboss 0
  • secondary metabolites 0
  • frame-shift correction 0
  • long-read sequencing 0
  • random forest 0
  • metagenomes 0
  • fetch 0
  • seqtk 0
  • vdj 0
  • varcal 0
  • cnv calling 0
  • ancient dna 0
  • CNV 0
  • Streptococcus pneumoniae 0
  • cvnkit 0
  • salmonella 0
  • estimation 0
  • single cells 0
  • calling 0
  • edit distance 0
  • recombination 0
  • genome bins 0
  • rename 0
  • eCLIP 0
  • sequenzautils 0
  • parse 0
  • transformation 0
  • find 0
  • authentication 0
  • immunoprofiling 0
  • blastn 0
  • settings 0
  • collate 0
  • dict 0
  • fixmate 0
  • proteome 0
  • HOPS 0
  • structural-variant calling 0
  • gene labels 0
  • fasterq-dump 0
  • sra-tools 0
  • screening 0
  • fusions 0
  • cleaning 0
  • correction 0
  • soft-clipped clusters 0
  • trgt 0
  • shigella 0
  • corrupted 0
  • switch 0
  • nacho 0
  • nanostring 0
  • mRNA 0
  • GEO 0
  • image_processing 0
  • MCMICRO 0
  • NRPS 0
  • de novo assembler 0
  • duplicate 0
  • panelofnormals 0
  • duplex 0
  • realignment 0
  • standardise 0
  • filtermutectcalls 0
  • RiPP 0
  • taxonomic profile 0
  • library 0
  • Read depth 0
  • merge mate pairs 0
  • preseq 0
  • normalize 0
  • Duplication purging 0
  • microbial 0
  • svdb 0
  • adapter 0
  • import 0
  • dereplicate 0
  • bayesian 0
  • deconvolution 0
  • antibiotics 0
  • purge duplications 0
  • reads merging 0
  • scaffold 0
  • UMIs 0
  • interval list 0
  • standardization 0
  • polish 0
  • gatk 0
  • joint genotyping 0
  • allele-specific 0
  • norm 0
  • scatter 0
  • reheader 0
  • bfiles 0
  • short reads 0
  • ome-tif 0
  • unaligned 0
  • taxon tables 0
  • small genome 0
  • repeats 0
  • standardisation 0
  • contig 0
  • otu tables 0
  • amp 0
  • error 0
  • readproteingroups 0
  • umicollapse 0
  • c to t 0
  • vcf2bed 0
  • de-novo 0
  • boxplot 0
  • shinyngs 0
  • proteus 0
  • antimicrobial peptide prediction 0
  • exploratory 0
  • longread 0
  • sha256 0
  • 256 bit 0
  • density 0
  • genepred 0
  • decompress 0
  • coding 0
  • transcroder 0
  • snakemake 0
  • cds 0
  • bam2seqz 0
  • workflow 0
  • workflow_mode 0
  • createreadcountpanelofnormals 0
  • gc_wiggle 0
  • Mycobacterium tuberculosis 0
  • copyratios 0
  • denoisereadcounts 0
  • freqsum 0
  • readwriter 0
  • dnamodelapply 0
  • eucaryotes 0
  • sequencing adapters 0
  • sliding 0
  • polya tail 0
  • rdtest 0
  • rare variants 0
  • eigenvectors 0
  • ucsc/liftover 0
  • gtftogenepred 0
  • fast5 0
  • refflat 0
  • bedtobigbed 0
  • AMPs 0
  • bigbed 0
  • relative coverage 0
  • bedgraphtobigwig 0
  • genetic sex 0
  • sex determination 0
  • induce 0
  • hicPCA 0
  • features 0
  • yahs 0
  • sliding window 0
  • subsample bam 0
  • usearch 0
  • maf 0
  • gemini 0
  • vcf2db 0
  • long read alignment 0
  • chromosomal rearrangements 0
  • invariant 0
  • ribosomal RNA 0
  • pangenome-scale 0
  • SNPs 0
  • downsample bam 0
  • downsample 0
  • snv 0
  • spatype 0
  • rRNA 0
  • lua 0
  • fracminhash sketch 0
  • vcfbreakmulti 0
  • uniq 0
  • deduplicate 0
  • VCFtools 0
  • verifybamid 0
  • DNA contamination estimation 0
  • construct 0
  • toml 0
  • hash sketch 0
  • graph projection to vcf 0
  • extractunbinned 0
  • linkbins 0
  • signatures 0
  • sintax 0
  • vsearch/sort 0
  • spa 0
  • all versus all 0
  • rdtest2vcf 0
  • CRAM 0
  • gender determination 0
  • SMN2 0
  • SMN1 0
  • copy number alterations 0
  • files 0
  • copy number variation 0
  • geo 0
  • copy number analysis 0
  • mapad 0
  • svtk/baftest 0
  • adna 0
  • baftest 0
  • countsvtypes 0
  • scRNA-Seq 0
  • POA 0
  • copy-number 0
  • mashmap 0
  • upd 0
  • streptococcus 0
  • sccmec 0
  • variantcalling 0
  • wavefront 0
  • disomy 0
  • dist 0
  • sniffles 0
  • detecting svs 0
  • whamg 0
  • snippy 0
  • wham 0
  • short-read sequencing 0
  • core 0
  • model 0
  • constant 0
  • resistance genes 0
  • dnascope 0
  • haplotag 0
  • drug categorization 0
  • uniques 0
  • Illumina 0
  • functional 0
  • impute-info 0
  • tags 0
  • tag2tag 0
  • hashing-based deconvolution 0
  • rank 0
  • java 0
  • script 0
  • xml 0
  • svg 0
  • standard 0
  • staging 0
  • Read trimming 0
  • Staging 0
  • admixture 0
  • microRNA 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
  • Read report 0
  • Read filters 0
  • ATACshift 0
  • cellsnp 0
  • trimfq 0
  • vcflib/vcffixup 0
  • AC/NS/AF 0
  • Pacbio 0
  • guidetree 0
  • bwamem2 0
  • bwameme 0
  • grabix 0
  • ribosomal 0
  • 10x 0
  • regulatory network 0
  • transcription factors 0
  • paraphase 0
  • cram-size 0
  • nanoq 0
  • size 0
  • quality check 0
  • realign 0
  • circular 0
  • spot 0
  • orthogroup 0
  • orthologs 0
  • sage 0
  • mass spectrometry 0
  • featuretable 0
  • extraction 0
  • cgMLST 0
  • WGS 0
  • redundant 0
  • shift 0
  • setgt 0
  • genotype-based demultiplexing 0
  • updatedata 0
  • metagenome assembler 0
  • scanpy 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
  • run 0
  • chip 0
  • decontamination 0
  • partitioning 0
  • malformed 0
  • fix 0
  • paired reads re-pairing 0
  • regex 0
  • patterns 0
  • Immune Deconvolution 0
  • Bioinformatics Tools 0
  • Computational Immunology 0
  • catpack 0
  • prepare 0
  • mzML 0
  • taxonomic composition 0
  • human removal 0
  • hostile 0
  • jvarkit 0
  • adapterremoval 0
  • translate 0
  • tar 0
  • tarball 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
  • antimicrobial reistance 0
  • morphology 0
  • barcodes 0
  • subsetting 0
  • logFC 0
  • significance statistic 0
  • p-value 0
  • import segmentation 0
  • nuclear segmentation 0
  • cell segmentation 0
  • contiguate 0
  • relabel 0
  • resegment 0
  • donor deconvolution 0
  • lexogen 0
  • groupby 0
  • idx 0
  • Staphylococcus aureus 0
  • structural variant 0
  • bam2fastx 0
  • bam2fastq 0
  • immcantation 0
  • airrseq 0
  • immunoinformatics 0
  • co-orthology 0
  • homology 0
  • sequence similarity 0
  • spectral clustering 0
  • comparative genomics 0
  • deep variant 0
  • mutect 0
  • transform 0
  • gost 0
  • gaps 0
  • introns 0
  • install 0
  • joint-genotyping 0
  • genotypegvcf 0
  • affy 0
  • parallel 0
  • plastid 0
  • resfinder 0
  • pseudohaploid 0
  • raw 0
  • mgf 0
  • parquet 0
  • parser 0
  • rad 0
  • gprofiler2 0
  • standardize 0
  • hmmfetch 0
  • tnscope 0
  • bgen 0
  • chloroplast 0
  • confidence 0
  • blat 0
  • alr 0
  • clr 0
  • boxcox 0
  • genetic 0
  • Escherichia coli 0
  • propd 0
  • Read coverage histogram 0
  • reverse complement 0
  • simulation 0
  • decompose 0
  • vector 0
  • transmembrane 0
  • genome graph 0
  • tnseq 0
  • decoy 0
  • htseq 0
  • rrna 0
  • sompy 0
  • peak picking 0
  • site frequency spectrum 0
  • ancestral alleles 0
  • derived alleles 0
  • tnfilter 0
  • array_cgh 0
  • cytosure 0
  • dbsnp 0
  • quarto 0
  • droplet based single cells 0
  • grea 0
  • Bayesian 0
  • structural-variants 0
  • omics 0
  • biological activity 0
  • prior knowledge 0
  • tag 0
  • cell_barcodes 0
  • mygene 0
  • go 0
  • pile up 0
  • nanopore sequencing 0
  • rna velocity 0
  • cobra 0
  • extension 0
  • functional enrichment 0
  • spatial_neighborhoods 0
  • translation 0
  • paired reads merging 0
  • overlap-based merging 0
  • check 0
  • hamming-distance 0
  • hashing-based deconvoltion 0
  • gnu 0
  • coreutils 0
  • generic 0
  • transposable element 0
  • retrieval 0
  • MMseqs2 0
  • InterProScan 0
  • busco 0
  • scimap 0
  • associations 0
  • python 0
  • hwe statistics 0
  • r 0
  • coexpression 0
  • correlation 0
  • corpcor 0
  • assay 0
  • phylogenetics 0
  • minimum_evolution 0
  • distance-based 0
  • nucleotide sequence 0
  • homologs 0
  • multi-tool 0
  • reference panels 0
  • hardy-weinberg 0
  • hwe equilibrium 0
  • case/control 0
  • reference-independent 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
  • clahe 0
  • refresh 0
  • association 0
  • GWAS 0
  • pseudodiploid 0
  • gfastats 0
  • random draw 0
  • selectvariants 0
  • indexfeaturefile 0
  • csi 0
  • learnreadorientationmodel 0
  • readorientationartifacts 0
  • leftalignandtrimvariants 0
  • mergebamalignment 0
  • mutectstats 0
  • snvs 0
  • postprocessgermlinecnvcalls 0
  • preprocessintervals 0
  • printreads 0
  • printsvevidence 0
  • reblockgvcf 0
  • revert 0
  • shiftchain 0
  • getpileupsumaries 0
  • shiftfasta 0
  • shiftintervals 0
  • site depth 0
  • splitcram 0
  • splitintervals 0
  • svannotate 0
  • svcluster 0
  • variantfiltration 0
  • recalibration model 0
  • variantrecalibrator 0
  • gawk 0
  • txt 0
  • file parsing 0
  • bgc 0
  • readcountssummary 0
  • germlinevariantsites 0
  • deduping 0
  • condensedepthevidence 0
  • vqsr 0
  • asereadcounter 0
  • bedtointervallist 0
  • calculatecontamination 0
  • cross-samplecontamination 0
  • getpileupsummaries 0
  • calibratedragstrmodel 0
  • cnnscorevariants 0
  • collectreadcounts 0
  • collectsvevidence 0
  • combinegvcfs 0
  • short variant discovery 0
  • composestrtablefile 0
  • dragstr 0
  • createsequencedictionary 0
  • germlinecnvcaller 0
  • createsomaticpanelofnormals 0
  • BCF 0
  • determinegermlinecontigploidy 0
  • duplication metrics 0
  • estimatelibrarycomplexity 0
  • filterintervals 0
  • filtervarianttranches 0
  • tranche filtering 0
  • gatherbqsrreports 0
  • genomicsdb 0
  • genomicsdbimport 0
  • jointgenotyping 0
  • panelofnormalscreation 0
  • germline contig ploidy 0
  • genome profile 0
  • compound 0
  • annotateintervals 0
  • mitochondrial 0
  • gunc 0
  • gunzip 0
  • yaml 0
  • gvcftools 0
  • extract_variants 0
  • extractvariants 0
  • bamtools/convert 0
  • abricate 0
  • amrfinderplus 0
  • fARGene 0
  • rgi 0
  • ibd 0
  • hbd 0
  • beagle 0
  • mouse 0
  • genome taxonomy database 0
  • Haemophilus influenzae 0
  • haplotype resolution 0
  • gccounter 0
  • readcounter 0
  • reformat 0
  • HMMER 0
  • amino acid 0
  • Hidden Markov Model 0
  • hmtnote 0
  • annotations 0
  • pos 0
  • haemophilus 0
  • panel_of_normals 0
  • IDR 0
  • archaea 0
  • bamtools/split 0
  • models 0
  • background_correction 0
  • smaller fastqs 0
  • genome size 0
  • genome heterozygosity 0
  • repeat content 0
  • Salmonella Typhi 0
  • Mykrobe 0
  • clumping fastqs 0
  • chromap 0
  • genome summary 0
  • genome manipulation 0
  • genome statistics 0
  • microscopy 0
  • gget 0
  • low coverage 0
  • illumiation_correction 0
  • GTDB taxonomy 0
  • trimBam 0
  • gstama/polyacleanup 0
  • gstama/merge 0
  • TAMA 0
  • gene model 0
  • tama_collapse.py 0
  • bamUtil 0
  • element 0
  • Sample 0
  • genomes on a tree 0
  • merge compare 0
  • GNU 0
  • joint-variant-calling 0
  • Imputation 0
  • Haplotypes 0
  • variant quality score recalibration 0
  • targets 0
  • igv.js 0
  • postprocessing 0
  • Segmentation 0
  • Cores 0
  • Assembly 0
  • custom 0
  • version 0
  • domains 0
  • na 0
  • compartments 0
  • topology 0
  • cls 0
  • calder2 0
  • gct 0
  • cutesv 0
  • cadd 0
  • pcr duplicates 0
  • UNet 0
  • paired-end 0
  • tblastn 0
  • subtyping 0
  • track 0
  • Salmonella enterica 0
  • corrrelation 0
  • scatterplot 0
  • sorted 0
  • cumulative coverage 0
  • file manipulation 0
  • bioawk 0
  • unionBedGraphs 0
  • blastx 0
  • segment 0
  • TMA dearray 0
  • mcool 0
  • duphold 0
  • crispr 0
  • duplicate removal 0
  • chromosome_visualization 0
  • splice 0
  • quality assurnce 0
  • qa 0
  • polymut 0
  • polymorphic 0
  • polymorphic sites 0
  • protein coding genes 0
  • cmseq 0
  • access 0
  • antitarget 0
  • export 0
  • target 0
  • antibody capture 0
  • genomic bins 0
  • antigen capture 0
  • partition histograms 0
  • multiomics 0
  • concoct 0
  • nucleotide composition 0
  • subcontigs 0
  • mkvdjref 0
  • cellpose 0
  • cooler/balance 0
  • cload 0
  • digest 0
  • enzyme 0
  • hifi 0
  • makebins 0
  • subtract 0
  • structural variation 0
  • heattree 0
  • random 0
  • ENA 0
  • public 0
  • closest 0
  • consensus sequence 0
  • duplexumi 0
  • groupreads 0
  • unmapped 0
  • ubam 0
  • zipperbams 0
  • bamtobed 0
  • sorting 0
  • autozygosity 0
  • single molecule 0
  • generate 0
  • homozygosity 0
  • genomecov 0
  • lint 0
  • fq 0
  • rust 0
  • variant caller 0
  • biallelic 0
  • somatic variant calling 0
  • germline variant calling 0
  • bacterial variant calling 0
  • bootstrapping 0
  • UShER 0
  • gamma 0
  • gene-calling 0
  • gangstr 0
  • update header 0
  • SRA 0
  • getfasta 0
  • depth information 0
  • split by chromosome 0
  • escherichia coli 0
  • slopBed 0
  • PEP 0
  • schema 0
  • pep 0
  • eigenstratdatabasetools 0
  • bases 0
  • sizes 0
  • eklipse 0
  • region 0
  • shiftBed 0
  • circos 0
  • deletion 0
  • multinterval 0
  • overlapped bed 0
  • ANI 0
  • chunking 0
  • ARGs 0
  • antibiotic resistance genes 0
  • faqcs 0
  • str 0
  • overlap 0
  • jaccard 0
  • maskfasta 0
  • embl 0
  • cache 0
  • percent on target 0
  • endogenous DNA 0
  • Streptococcus pyogenes 0
  • swissprot 0
  • genbank 0
  • igv 0
  • js 0
  • selection 0
  • identifiers 0
  • NETCAGE 0
  • RAMPAGE 0
  • csRNA-seq 0
  • STRIPE-seq 0
  • PRO-seq 0
  • GRO-seq 0
  • HLA 0
  • exclude 0
  • variant identifiers 0
  • subset 0
  • indep 0
  • indep pairwise 0
  • recode 0
  • whole genome association 0
  • scoring 0
  • PRO-cap 0
  • variant genetic 0
  • pmdtools 0
  • porechop_abi 0
  • contact 0
  • pretext 0
  • jpg 0
  • bmp 0
  • contact maps 0
  • gene finding 0
  • intervals coverage 0
  • genomic intervals 0
  • normal database 0
  • panel of normals 0
  • cutoff 0
  • CAGE 0
  • GRO-cap 0
  • duplicate purging 0
  • motif 0
  • pairstools 0
  • restriction fragments 0
  • select 0
  • http(s) 0
  • paragraph 0
  • graphs 0
  • pbbam 0
  • pbmerge 0
  • subreads 0
  • pbp 0
  • pair-end 0
  • read 0
  • pedigrees 0
  • utility 0
  • ChIP-Seq 0
  • CoPRO 0
  • phantom peaks 0
  • prophage 0
  • identification 0
  • illumina datasets 0
  • phylogenetic composition 0
  • hybrid-selection 0
  • mate-pair 0
  • liftovervcf 0
  • pcr 0
  • picard/renamesampleinvcf 0
  • sortvcf 0
  • deletions 0
  • insertions 0
  • tandem duplications 0
  • haplotype purging 0
  • false duplications 0
  • ligation junctions 0
  • cut&tag 0
  • calmd 0
  • faidx 0
  • insert size 0
  • repair 0
  • paired 0
  • read pairs 0
  • doCounts 0
  • readgroup 0
  • allele counts 0
  • nuclear contamination estimate 0
  • scramble 0
  • cluster analysis 0
  • clusteridentifier 0
  • peak-caller 0
  • cut&run 0
  • ampliconclip 0
  • chromatin 0
  • seacr 0
  • assembly-binning 0
  • applyvarcal 0
  • VQSR 0
  • variant recalibration 0
  • post Post-processing 0
  • subseq 0
  • grep 0
  • sequence headers 0
  • sertotype 0
  • interleave 0
  • header 0
  • seq 0
  • installation 0
  • amplicon 0
  • assembly curation 0
  • fragment_size 0
  • Haplotype purging 0
  • False duplications 0
  • Assembly curation 0
  • purging 0
  • quast 0
  • neighbour-joining 0
  • subsampling 0
  • long uncorrected reads 0
  • rhocall 0
  • R 0
  • bamstat 0
  • strandedness 0
  • experiment 0
  • read_pairs 0
  • inner_distance 0
  • duplicate marking 0
  • salsa 0
  • sambamba 0
  • flagstat 0
  • multimapper 0
  • Ancestor 0
  • LCA 0
  • salsa2 0
  • rtg-tools 0
  • read distribution 0
  • rocplot 0
  • pedfilter 0
  • rtg 0
  • integrity 0
  • mapping-based 0
  • sequence-based 0
  • pairtools 0
  • upper-triangular matrix 0
  • genome browser 0
  • sgRNA 0
  • cycif 0
  • legionella 0
  • clinical 0
  • pneumophila 0
  • limma 0
  • Listeria monocytogenes 0
  • background 0
  • lofreq/call 0
  • lofreq/filter 0
  • qualities 0
  • AMP 0
  • peptide prediction 0
  • single-stranded 0
  • functional genomics 0
  • CRISPR-Cas9 0
  • adapter removal 0
  • maximum-likelihood 0
  • rra 0
  • ancientDNA 0
  • DNA damage 0
  • NGS 0
  • damage patterns 0
  • estimate 0
  • authentict 0
  • taxonomic assignment 0
  • mash/sketch 0
  • reduced 0
  • representations 0
  • maxbin2 0
  • read group 0
  • collapsing 0
  • train 0
  • bias 0
  • papermill 0
  • multicut 0
  • pixel classification 0
  • pixel_classification 0
  • probability_maps 0
  • population genomics 0
  • genomic islands 0
  • insertion 0
  • bacphlip 0
  • jasminesv 0
  • jasmine 0
  • Python 0
  • Jupyter 0
  • jupytext 0
  • virulent 0
  • spliced 0
  • temperate 0
  • kallisto/index 0
  • quant 0
  • lifestyle 0
  • digital normalization 0
  • k-mer counting 0
  • effective genome size 0
  • Klebsiella 0
  • pneumoniae 0
  • kegg 0
  • kofamscan 0
  • combining 0
  • autofluorescence 0
  • reorder 0
  • metagenome-assembled genomes 0
  • mass-spectroscopy 0
  • flip 0
  • gender 0
  • ratio 0
  • mitochondrial to nuclear ratio 0
  • bioinformatics tools 0
  • Beautiful stand-alone HTML report 0
  • GATK UnifiedGenotyper 0
  • SNP table 0
  • contaminant 0
  • cancer genome 0
  • somatic structural variations 0
  • mobile element insertions 0
  • sequencing summary 0
  • NextGenMap 0
  • ngm 0
  • Neisseria gonorrhoeae 0
  • graph construction 0
  • scan 0
  • graph drawing 0
  • squeeze 0
  • odgi 0
  • combine graphs 0
  • graph stats 0
  • graph unchopping 0
  • graph formats 0
  • graph viz 0
  • tumor/normal 0
  • hla-typing 0
  • ILP 0
  • HLA-I 0
  • block-compressed 0
  • PCR/optical duplicates 0
  • mtnucratio 0
  • microsatellite instability 0
  • ATLAS 0
  • post mortem damage 0
  • mcr-1 0
  • MD5 0
  • 128 bit 0
  • megahit 0
  • denovo 0
  • debruijn 0
  • daa 0
  • rma6 0
  • Neisseria meningitidis 0
  • sequencing_bias 0
  • k-mer frequency 0
  • 3D heat map 0
  • contour map 0
  • Merqury 0
  • assembly evaluation 0
  • otu table 0
  • atlas 0
  • mosdepth 0
  • reference genome 0
  • mitochondrial genome 0
  • target prediction 0
  • mkarv 0
  • microrna 0
  • de Bruijn 0
  • smudgeplot 0
  • assembler 0
  • mbias 0
  • methylation bias 0
  • metaphlan 0
  • unionsum 0
  • ploidy 0
  • uniparental 0

Doublet detection in single-cell RNA-seq data

01

h5ad predictions versions

Produces protein annotations and predictions from an amino acids FASTA file

010

tsv xml gff3 json versions

AMR predictions for supported species

010

csv json versions

mykrobe:

Antibiotic resistance prediction in minutes

Quality control of riboseq bam data

012012012010101

predictions all transprofile versions

ribotish:

Ribo TIS Hunter (Ribo-TISH) identifies translation activities using ribosome profiling data.

Module to use scds for doublet scoring

01

rds predictions versions

Detect doublets in single-cell RNA-Seq data

01

h5ad predictions versions

scvitools:

A scalable toolkit for probabilistic modeling applied to single-cell omics data

The dbNSFP is an integrated database of functional predictions from multiple algorithms

012012

vcf versions

snpsift:

SnpSift is a toolbox that allows you to filter and manipulate annotated files

Transcript Selector for BRAKER TSEBRA combines gene predictions by selecting transcripts based on their extrisic evidence support

01000

tsebra_gtf tsebra_scores versions

Click here to trigger an update.