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.

  • antimicrobial peptides 6
  • proteomics 5
  • openms 5
  • align 4
  • reporting 4
  • amps 4
  • ampir 4
  • parsing 4
  • hmmsearch 3
  • idXML 3
  • DRAMP 3
  • amplify 3
  • macrel 3
  • neubi 3
  • filter 2
  • gff 2
  • ampgram 2
  • amptransformer 2
  • format 2
  • eido 2
  • fasta 1
  • database 1
  • convert 1
  • clustering 1
  • contigs 1
  • mmseqs2 1
  • transcript 1
  • prediction 1
  • eukaryotes 1
  • score 1
  • genome mining 1
  • validate 1
  • samplesheet 1
  • metagenomic 1
  • identifier 1
  • metagenomes 1
  • switch 1
  • amp 1
  • antimicrobial peptide prediction 1
  • coding 1
  • transcroder 1
  • cds 1
  • eucaryotes 1
  • AMPs 1
  • model 1
  • mzML 1
  • decoy 1
  • MMseqs2 1
  • InterProScan 1
  • refresh 1
  • PEP 1
  • schema 1
  • pep 1
  • ARGs 1
  • antibiotic resistance genes 1
  • AMP 1
  • peptide prediction 1
  • bam 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
  • merge 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
  • conversion 0
  • quality 0
  • binning 0
  • count 0
  • VCF 0
  • ancient DNA 0
  • single-cell 0
  • copy number 0
  • phylogeny 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
  • illumina 0
  • compression 0
  • picard 0
  • cna 0
  • bqsr 0
  • methylseq 0
  • kmer 0
  • rnaseq 0
  • protein 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
  • tsv 0
  • visualisation 0
  • antimicrobial resistance 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
  • 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
  • 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
  • gene 0
  • decompression 0
  • msa 0
  • evaluation 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
  • single cell 0
  • mutect2 0
  • counts 0
  • cat 0
  • benchmark 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
  • riboseq 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
  • DNA sequence 0
  • abundance 0
  • ancestry 0
  • BGC 0
  • resistance 0
  • biosynthetic gene cluster 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
  • bamtools 0
  • vrhyme 0
  • complement 0
  • fastk 0
  • miRNA 0
  • pileup 0
  • chimeras 0
  • atac-seq 0
  • relatedness 0
  • spaceranger 0
  • dna 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
  • spark 0
  • roh 0
  • zip 0
  • unzip 0
  • indel 0
  • uncompress 0
  • long_read 0
  • replace 0
  • RNA-seq 0
  • prokaryotes 0
  • quality trimming 0
  • prokka 0
  • insert 0
  • untar 0
  • RNA 0
  • remove 0
  • rna_structure 0
  • popscle 0
  • transcriptomics 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • variant pruning 0
  • antismash 0
  • effect prediction 0
  • scaffolding 0
  • pharmacogenetics 0
  • cancer genomics 0
  • snpsift 0
  • snpeff 0
  • blastp 0
  • eigenstrat 0
  • deseq2 0
  • rna-seq 0
  • doublets 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
  • 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
  • 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
  • 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
  • evidence 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
  • error 0
  • readproteingroups 0
  • umicollapse 0
  • c to t 0
  • vcf2bed 0
  • de-novo 0
  • boxplot 0
  • shinyngs 0
  • proteus 0
  • exploratory 0
  • longread 0
  • sha256 0
  • 256 bit 0
  • density 0
  • genepred 0
  • decompress 0
  • snakemake 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
  • 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
  • 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
  • predictions 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
  • dbnsfp 0
  • wavefront 0
  • disomy 0
  • dist 0
  • sniffles 0
  • detecting svs 0
  • whamg 0
  • snippy 0
  • wham 0
  • short-read sequencing 0
  • core 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
  • selector 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
  • doublet 0
  • Immune Deconvolution 0
  • Bioinformatics Tools 0
  • Computational Immunology 0
  • catpack 0
  • prepare 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
  • doublet_detection 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
  • 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
  • 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
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  • bamtools/convert 0
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  • pos 0
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  • bamtools/split 0
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  • element 0
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  • antibody capture 0
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  • closest 0
  • consensus sequence 0
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  • variant caller 0
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  • somatic variant calling 0
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A tool to parse and summarise results from antimicrobial peptides tools and present functional classification.

0100

sample_dir txt csv faa summary_csv summary_html log results_db results_db_dmnd results_db_fasta results_db_tsv versions

A submodule that clusters the merged AMP hits generated from ampcombi2/parsetables and ampcombi2/complete using MMseqs2 cluster.

0

cluster_tsv rep_cluster_tsv log versions

ampcombi2/cluster:

A tool for clustering all AMP hits found across many samples and supporting many AMP prediction tools.

A submodule that merges all output summary tables from ampcombi/parsetables in one summary file.

0

tsv log versions

ampcombi2/complete:

This merges the per sample AMPcombi summaries generated by running 'ampcombi2/parsetables'.

A submodule that parses and standardizes the results from various antimicrobial peptide identification tools.

0100000

sample_dir contig_gbks db_tsv tsv faa sample_log full_log db db_txt db_fasta db_mmseqs versions

ampcombi2/parsetables:

A parsing tool to convert and summarise the outputs from multiple AMP detection tools in a standardized format.

A fast and user-friendly method to predict antimicrobial peptides (AMPs) from any given size protein dataset. ampir uses a supervised statistical machine learning approach to predict AMPs.

01000

amps_faa amps_tsv versions

AMPlify is an attentive deep learning model for antimicrobial peptide prediction.

010

tsv versions

amplify:

Attentive deep learning model for antimicrobial peptide prediction

Convert any PEP project or Nextflow samplesheet to any format

000

versions samplesheet_converted

eido:

Convert any PEP project or Nextflow samplesheet to any format

Validate samplesheet or PEP config against a schema

000

versions log

validate:

Validate samplesheet or PEP config against a schema.

tool that takes either fragmented metagenomic data or longer sequences as input and predicts and delivers full-length antiobiotic resistance genes as output.

010

log txt hmm hmm_genes orfs orfs_amino contigs contigs_pept filtered filtered_pept fragments trimmed spades metagenome tmp versions

A tool that mines antimicrobial peptides (AMPs) from (meta)genomes by predicting peptides from genomes (provided as contigs) and outputs all the predicted anti-microbial peptides found.

01

smorfs all_orfs amp_prediction readme_file log_file versions

macrel:

A pipeline for AMP (antimicrobial peptide) prediction

Create a decoy peptide database from a standard FASTA database.

01

decoy_fasta versions

openms:

OpenMS is an open-source software C++ library for LC-MS data management and analyses

Filters peptide/protein identification results by different criteria.

01

mzml featurexml consensusxml versions

openms:

OpenMS is an open-source software C++ library for LC-MS data management and analyses

Filters peptide/protein identification results by different criteria.

012

filtered versions

openms:

OpenMS is an open-source software C++ library for LC-MS data management and analyses

Switches between different scores of peptide or protein hits in identification data

01

idxml versions

openms:

OpenMS is an open-source software C++ library for LC-MS data management and analyses

Refreshes the protein references for all peptide hits.

0101

id_file_pi versions

openms:

OpenMS is an open-source software C++ library for LC-MS data management and analyses

TransDecoder identifies candidate coding regions within transcript sequences. it is used to build gff file.

01

pep gff3 cds dat folder versions

transdecoder:

TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks.

TransDecoder identifies candidate coding regions within transcript sequences. It is used to build gff file. You can use this module after transdecoder_longorf

010

pep gff3 cds bed versions

transdecoder:

TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks.

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