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.

  • fasta 2
  • simulate 2
  • vcf 1
  • fastq 1
  • structural variants 1
  • sv 1
  • illumina 1
  • rnaseq 1
  • genotype 1
  • phasing 1
  • differential 1
  • riboseq 1
  • reads 1
  • switch 1
  • simulation 1
  • translation 1
  • error 1
  • bam 0
  • genomics 0
  • metagenomics 0
  • genome 0
  • index 0
  • alignment 0
  • reference 0
  • assembly 0
  • bed 0
  • gatk4 0
  • cram 0
  • sort 0
  • sam 0
  • variant calling 0
  • annotation 0
  • database 0
  • align 0
  • merge 0
  • filter 0
  • gff 0
  • bacteria 0
  • map 0
  • statistics 0
  • coverage 0
  • qc 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
  • count 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
  • bcftools 0
  • bisulfite 0
  • variation graph 0
  • reporting 0
  • bqsr 0
  • table 0
  • long-read 0
  • picard 0
  • indexing 0
  • wgs 0
  • databases 0
  • cna 0
  • consensus 0
  • bisulphite 0
  • QC 0
  • methylseq 0
  • protein 0
  • methylation 0
  • compression 0
  • stats 0
  • visualisation 0
  • serotype 0
  • phage 0
  • openms 0
  • metrics 0
  • tsv 0
  • imaging 0
  • demultiplex 0
  • 5mC 0
  • taxonomic classification 0
  • antimicrobial resistance 0
  • sequences 0
  • mapping 0
  • depth 0
  • bins 0
  • cluster 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
  • 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
  • spatial 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
  • mkref 0
  • peaks 0
  • msa 0
  • hmmer 0
  • seqkit 0
  • complexity 0
  • example 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
  • mirna 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
  • 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
  • miRNA 0
  • C to T 0
  • bwameth 0
  • amplicon sequences 0
  • fusion 0
  • chimeras 0
  • spaceranger 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
  • smrnaseq 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
  • 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
  • mRNA 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
  • nacho 0
  • mudskipper 0
  • read-group 0
  • standardisation 0
  • ped 0
  • xz 0
  • nanostring 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
  • 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
  • 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
  • microRNA 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
  • parquet 0
  • parser 0
  • dbsnp 0
  • standardize 0
  • bamtools/split 0
  • quarto 0
  • python 0
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  • correlation 0
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  • check 0
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  • generic 0
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  • retrieval 0
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  • sequencing_bias 0
  • MMseqs2 0
  • hash sketch 0
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  • targets 0
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  • metagenome-assembled genomes 0
  • gamma 0
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  • Klebsiella 0
  • pneumoniae 0
  • condensedepthevidence 0
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  • combinegvcfs 0
  • collectsvevidence 0
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  • bedtointervallist 0
  • reorder 0
  • spliced 0
  • train 0
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  • 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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  • scan 0
  • random 0
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  • ratio 0
  • mitochondrial to nuclear ratio 0
  • bioinformatics tools 0
  • Beautiful stand-alone HTML report 0
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  • contaminant 0
  • public 0
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  • 128 bit 0
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  • denovo 0
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  • lint 0
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  • de Bruijn 0
  • effective genome size 0
  • createsequencedictionary 0
  • ngm 0
  • extract_variants 0
  • svcluster 0
  • svannotate 0
  • gstama/polyacleanup 0
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  • site depth 0
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  • extractvariants 0
  • variantfiltration 0
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  • beagle 0
  • mitochondrial 0
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  • selectvariants 0
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  • TAMA 0
  • revert 0
  • genome profile 0
  • Mykrobe 0
  • genome summary 0
  • genome manipulation 0
  • genome statistics 0
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  • Haplotypes 0
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  • txt 0
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  • panelofnormalscreation 0
  • genomic islands 0
  • insertion 0
  • jointgenotyping 0
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  • Python 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

Simulation tool to generate synthetic Illumina next-generation sequencing reads

01000

fastq aln sam versions

art:

ART is a set of simulation tools to generate synthetic next-generation sequencing reads. ART simulates sequencing reads by mimicking real sequencing process with empirical error models or quality profiles summarized from large recalibrated sequencing data. ART can also simulate reads using user own read error model or quality profiles.

Program to compute switch error rate and genotyping error rate given simulated or trio data.

01234012012

errors versions

shapeit5:

Fast and accurate method for estimation of haplotypes (phasing)

Simulate an SV VCF file based on a reference genome

01010100

parameters vcf bed fasta insertions versions

survivor:

Toolset for SV simulation, comparison and filtering

simulating sequence reads from a reference genome

01

fastq versions

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