# Galaxy Skills — Curated Tool Profiles

**200 tools** profiled from usegalaxy.org.

| Tool | Category | Description |
|------|----------|-------------|
| [Augustus](augustus.md) | Annotation | gene prediction for prokaryotic and eukaryotic genomes |
| [Bakta](bakta.md) | Annotation | Rapid and standardized annotation of bacterial genomes, MAGs |
| [Maker](maker.md) | Annotation | genome annotation pipeline |
| [Prokka](prokka.md) | Annotation | prokaryotic genome annotation |
| [Bandage Image](bandage-image.md) | Assembly | visualize de novo assembly graphs |
| [Bandage Info](bandage-info.md) | Assembly | determine statistics of de novo assembly graphs |
| [Bionano Hybrid Scaffold](bionano-hybrid-scaffold.md) | Assembly | automates the scaffolding process |
| [Create assemblies with Unicycler](create-assemblies-with-unicycler.md) | Assembly |  |
| [Hifiasm](hifiasm.md) | Assembly | haplotype-resolved de novo assembler for PacBio Hifi reads |
| [MEGAHIT](megahit.md) | Assembly | for metagenomics assembly |
| [Pretext Snapshot](pretext-snapshot.md) | Assembly | image generator for Pretext contact maps |
| [PretextMap](pretextmap.md) | Assembly | converts SAM or BAM files into genome contact maps |
| [Purge overlaps](purge-overlaps.md) | Assembly | and haplotigs in an assembly based on read depth (purge_dups |
| [Quast](quast.md) | Assembly | Genome assembly Quality |
| [Racon](racon.md) | Assembly | Consensus module for raw de novo DNA assembly of long uncorr |
| [SALSA](salsa.md) | Assembly | scaffold long read assemblies with Hi-C |
| [SPAdes](spades.md) | Assembly | genome assembler for genomes of regular and single-cell proj |
| [Shovill](shovill.md) | Assembly | Faster SPAdes assembly of Illumina reads |
| [VelvetOptimiser](velvetoptimiser.md) | Assembly | Automatically optimize Velvet assemblies |
| [miniasm](miniasm.md) | Assembly | Ultrafast de novo assembly for long noisy reads |
| [rnaSPAdes](rnaspades.md) | Assembly | assembler for RNA-Seq data |
| [velvetg](velvetg.md) | Assembly | Velvet sequence assembler for very short reads |
| [velveth](velveth.md) | Assembly | Prepare a dataset for the Velvet velvetg Assembler |
| [BAM filter](bam-filter.md) | ChIP-seq | Removes reads from a BAM file based on criteria |
| [DiffBind](diffbind.md) | ChIP-seq | differential binding analysis of ChIP-Seq peak data |
| [MACS2 bdgpeakcall](macs2-bdgpeakcall.md) | ChIP-seq | Call peaks from bedGraph output |
| [MACS2 callpeak](macs2-callpeak.md) | ChIP-seq | Call peaks from alignment results |
| [MACS2 predictd](macs2-predictd.md) | ChIP-seq | Predict 'd' or fragment size from alignment results |
| [SEACR](seacr.md) | ChIP-seq | for sparse enrichment analysis |
| [IQ-TREE](iq-tree.md) | Evolution | Phylogenomic / evolutionary tree construction from multiple  |
| [Cutadapt](cutadapt.md) | FASTA/FASTQ | Remove adapter sequences from FASTQ/FASTA |
| [Fasta Statistics](fasta-statistics.md) | FASTA/FASTQ | display summary statistics for a FASTA file |
| [Gene length and GC content](gene-length-and-gc-content.md) | FASTA/FASTQ | from GTF and FASTA file |
| [Manipulate FASTQ](manipulate-fastq.md) | FASTA/FASTQ | reads on various attributes |
| [Trim Galore!](trim-galore.md) | FASTA/FASTQ | adaptive quality and adapter trimmer |
| [UMI-tools count](umi-tools-count.md) | FASTA/FASTQ | performs quantification of UMIs from BAM files |
| [UMI-tools deduplicate](umi-tools-deduplicate.md) | FASTA/FASTQ | Extract UMI from fastq files |
| [UMI-tools extract](umi-tools-extract.md) | FASTA/FASTQ | Extract UMI from fastq files |
| [UMI-tools whitelist](umi-tools-whitelist.md) | FASTA/FASTQ | Extract cell barcodes from FASTQ files |
| [faSplit](fasplit.md) | FASTA/FASTQ | Split a FASTA file |
| [fastp](fastp.md) | FASTA/FASTQ | - fast all-in-one preprocessing for FASTQ files |
| [filtlong](filtlong.md) | FASTA/FASTQ | Filtering long reads by quality |
| [Compute quality statistics](compute-quality-statistics.md) | FASTQ Quality Control |  |
| [Draw nucleotides distribution chart](draw-nucleotides-distribution-chart.md) | FASTQ Quality Control |  |
| [Draw quality score boxplot](draw-quality-score-boxplot.md) | FASTQ Quality Control |  |
| [FASTQ Summary Statistics](fastq-summary-statistics.md) | FASTQ Quality Control | by column |
| [FASTQ info](fastq-info.md) | FASTQ Quality Control | validates single or paired fastq files |
| [FASTQE](fastqe.md) | FASTQ Quality Control | visualize fastq files with emoji's 🧬😎 |
| [Falco](falco.md) | FASTQ Quality Control | An alternative, more performant implementation of FastQC for |
| [FastQC](fastqc.md) | FASTQ Quality Control | Read Quality reports |
| [MultiQC](multiqc.md) | FASTQ Quality Control | aggregate results from bioinformatics analyses into a single |
| [PRINSEQ](prinseq.md) | FASTQ Quality Control | to process quality of sequences |
| [Trimmomatic](trimmomatic.md) | FASTQ Quality Control | flexible read trimming tool for Illumina NGS data |
| [Phyogenetic reconstruction with RAxML](phyogenetic-reconstruction-with-raxml.md) | Genome Diversity | - Maximum Likelihood based inference of large phylogenetic t |
| [Circos: Alignments to links](circos-alignments-to-links.md) | Graph/Display Data | reformats alignment files to prepare for Circos |
| [Circos: Interval to Circos Text Labels](circos-interval-to-circos-text-labels.md) | Graph/Display Data | reformats interval files to prepare for Circos text labels |
| [Circos: Stack bigWigs as Histogram](circos-stack-bigwigs-as-histogram.md) | Graph/Display Data | reformats for use in Circos stacked histogram plots |
| [Circos: bigWig to Scatter](circos-bigwig-to-scatter.md) | Graph/Display Data | reformats bigWig files to prepare for Circos 2d scatter/line |
| [VCF to MAF Custom Track](vcf-to-maf-custom-track.md) | Graph/Display Data | for display at UCSC |
| [Align sequences](align-sequences.md) | Mapping | to a reference using a codon alignment algorithm |
| [BBTools: BBMap](bbtools-bbmap.md) | Mapping | short-read aligner |
| [BWA](bwa.md) | Mapping | - map short reads (< 100 bp) against reference genome |
| [BWA-MEM](bwa-mem.md) | Mapping | - map medium and long reads (> 100 bp) against reference gen |
| [BWA-MEM2](bwa-mem2.md) | Mapping | - map medium and long reads (> 100 bp) against reference gen |
| [Batched Lastz](batched-lastz.md) | Mapping | : align batches of sequences |
| [Bowtie2](bowtie2.md) | Mapping | - map reads against reference genome |
| [LASTZ](lastz.md) | Mapping | : align long sequences |
| [LASTZ_D](lastz-d.md) | Mapping | : estimate substitution scores matrix |
| [Map with minimap2](map-with-minimap2.md) | Mapping | A fast pairwise aligner for genomic and spliced nucleotide s |
| [MethylDackel](methyldackel.md) | Mapping | A tool for processing bisulfite sequencing alignments |
| [RNA STARSolo](rna-starsolo.md) | Mapping | mapping, demultiplexing and gene quantification for single c |
| [SegAlign](segalign.md) | Mapping | A Scalable GPU System for Pairwise Whole Genome Alignments b |
| [Winnowmap](winnowmap.md) | Mapping | a mapping tool optimized for repetitive sequences |
| [axtChain](axtchain.md) | Mapping | Chain together axt alignments |
| [bwameth](bwameth.md) | Mapping | Fast and accurate aligner of BS-Seq reads. |
| [chainPreNet](chainprenet.md) | Mapping | Remove chains that don't have a chance of being netted |
| [chainSort](chainsort.md) | Mapping | Sort chains |
| [metilene](metilene.md) | Mapping | calling differentially methylated regions from bisulfite seq |
| [Add metadata](add-metadata.md) | Metagenomic Analysis | to a BIOM table |
| [Bracken](bracken.md) | Metagenomic Analysis | to re-estimate abundance at a taxonomic level from kraken ou |
| [CAT add_names](cat-add-names.md) | Metagenomic Analysis | annotate with taxonomic names |
| [CAT bins](cat-bins.md) | Metagenomic Analysis | annotate with taxonomic classification |
| [CAT contigs](cat-contigs.md) | Metagenomic Analysis | annotate with taxonomic classification |
| [CAT prepare](cat-prepare.md) | Metagenomic Analysis | a database for CAT - Contig Annotation Tool |
| [CAT summarise](cat-summarise.md) | Metagenomic Analysis | the number of contigs or bins assigned to each taxonomic nam |
| [Convert](convert.md) | Metagenomic Analysis | between BIOM table formats |
| [Diamond](diamond.md) | Metagenomic Analysis | alignment tool for short sequences against a protein databas |
| [Diamond makedb](diamond-makedb.md) | Metagenomic Analysis | Build database from a FASTA file |
| [Diamond view](diamond-view.md) | Metagenomic Analysis | generate formatted output from DAA files |
| [HUMAnN](humann.md) | Metagenomic Analysis | to profile presence/absence and abundance of microbial pathw |
| [Kraken taxonomic report](kraken-taxonomic-report.md) | Metagenomic Analysis | view report of classification for multiple samples |
| [Kraken2](kraken2.md) | Metagenomic Analysis | assign taxonomic labels to sequencing reads |
| [MetaPhlAn](metaphlan.md) | Metagenomic Analysis | to profile the composition of microbial communities |
| [Nonpareil](nonpareil.md) | Metagenomic Analysis | to estimate average coverage and generate Nonpareil curves |
| [PlasFlow](plasflow.md) | Metagenomic Analysis | Prediction of plasmid sequences in metagenomic contigs |
| [VSearch alignment](vsearch-alignment.md) | Metagenomic Analysis |  |
| [VSearch chimera detection](vsearch-chimera-detection.md) | Metagenomic Analysis |  |
| [VSearch clustering](vsearch-clustering.md) | Metagenomic Analysis |  |
| [VSearch dereplication](vsearch-dereplication.md) | Metagenomic Analysis |  |
| [VSearch masking](vsearch-masking.md) | Metagenomic Analysis |  |
| [VSearch search](vsearch-search.md) | Metagenomic Analysis |  |
| [VSearch shuffling](vsearch-shuffling.md) | Metagenomic Analysis |  |
| [VSearch sorting](vsearch-sorting.md) | Metagenomic Analysis |  |
| [ClustalW](clustalw.md) | Multiple Alignments | multiple sequence alignment program for DNA or proteins |
| [DNAdiff](dnadiff.md) | Multiple Alignments | Evaluate similarities/differences between two sequences |
| [Delta-Filter](delta-filter.md) | Multiple Alignments | Filters alignment (delta) file from nucmer |
| [Extract MAF blocks](extract-maf-blocks.md) | Multiple Alignments | given a set of genomic intervals |
| [Kc-Align](kc-align.md) | Multiple Alignments |  |
| [MAF Coverage Stats](maf-coverage-stats.md) | Multiple Alignments | Alignment coverage information |
| [MAFFT](mafft.md) | Multiple Alignments | Multiple alignment program for amino acid or nucleotide sequ |
| [MAFFT add](mafft-add.md) | Multiple Alignments | Align a sequence,alignment or fragments to an existing align |
| [Mummer](mummer.md) | Multiple Alignments | Align two or more sequences |
| [Mummerplot](mummerplot.md) | Multiple Alignments | Generate 2-D dotplot of aligned sequences |
| [Nucmer](nucmer.md) | Multiple Alignments | Align two or more sequences |
| [Show-Coords](show-coords.md) | Multiple Alignments | Parse delta file and report coordinates and other informatio |
| [Clair3](clair3.md) | Nanopore | germline small variant caller for long-reads |
| [Flye assembly](flye-assembly.md) | Nanopore | of long and error-prone reads |
| [NanoPlot](nanoplot.md) | Nanopore | Plotting suite for Oxford Nanopore sequencing data and align |
| [Porechop](porechop.md) | Nanopore | adapter trimmer for Oxford Nanopore reads |
| [Pycoqc](pycoqc.md) | Nanopore | quality control for Nanopore sequencing data |
| [medaka consensus pipeline](medaka-consensus-pipeline.md) | Nanopore | Assembly polishing via neural networks |
| [medaka consensus tool](medaka-consensus-tool.md) | Nanopore | Assembly polishing via neural networks |
| [medaka variant pipeline](medaka-variant-pipeline.md) | Nanopore | via neural networks |
| [medaka variant tool](medaka-variant-tool.md) | Nanopore | Probability decoding |
| [DAVID](david.md) | Phenotype Association | functional annotation for a list of genes |
| [GPASS](gpass.md) | Phenotype Association | significant single-SNP associations in case-control studies |
| [LD](ld.md) | Phenotype Association | linkage disequilibrium and tag SNPs |
| [PASS](pass.md) | Phenotype Association | significant transcription factor binding sites from ChIP dat |
| [g:Profiler](g-profiler.md) | Phenotype Association | tools for functional profiling of gene lists |
| [plink](plink.md) | Phenotype Association | genome association analysis toolset |
| [MaxQuant](maxquant.md) | Proteomics |  |
| [Alleyoop](alleyoop.md) | RNA-seq | - post-processing and QC of Slamdunk analyses |
| [DESeq2](deseq2.md) | RNA-seq | Determines differentially expressed features from count tabl |
| [DEXSeq](dexseq.md) | RNA-seq | Determines differential exon usage from count tables |
| [DEXSeq-Count](dexseq-count.md) | RNA-seq | Prepare and count exon abundancies from RNA-seq data |
| [Generate gene to transcript map](generate-gene-to-transcript-map.md) | RNA-seq | for Trinity assembly |
| [HISAT2](hisat2.md) | RNA-seq | A fast and sensitive alignment program |
| [MiRDeep2](mirdeep2.md) | RNA-seq | identification of novel and known miRNAs |
| [MiRDeep2 Mapper](mirdeep2-mapper.md) | RNA-seq | process and map reads to a reference genome |
| [MiRDeep2 Quantifier](mirdeep2-quantifier.md) | RNA-seq | fast quantitation of reads mapping to known miRBase precurso |
| [Salmon quant](salmon-quant.md) | RNA-seq | Perform dual-phase, reads or mapping-based estimation of tra |
| [Seurat](seurat.md) | RNA-seq | - toolkit for exploration of single-cell RNA-seq data |
| [Slamdunk](slamdunk.md) | RNA-seq | - streamlining SLAM-seq analysis with ultra-high sensitivity |
| [StringTie](stringtie.md) | RNA-seq | transcript assembly and quantification |
| [StringTie merge](stringtie-merge.md) | RNA-seq | transcripts |
| [TransDecoder](transdecoder.md) | RNA-seq | finds coding regions within transcripts |
| [Trinity](trinity.md) | RNA-seq | de novo assembly of RNA-Seq data |
| [Trinotate](trinotate.md) | RNA-seq | functional transcript annotation |
| [edgeR](edger.md) | RNA-seq | Perform differential expression of count data |
| [featureCounts](featurecounts.md) | RNA-seq | Measure gene expression in RNA-Seq experiments from SAM or B |
| [htseq-count](htseq-count.md) | RNA-seq | - Count aligned reads in a BAM file that overlap features in |
| [limma](limma.md) | RNA-seq | Perform differential expression with limma-voom or limma-tre |
| [maSigPro](masigpro.md) | RNA-seq | Significant Gene Expression Profile Differences in Time Cour |
| [tximport](tximport.md) | RNA-seq | Summarize transcript-level estimates for gene-level analysis |
| [Convert, Merge, Randomize](convert-merge-randomize.md) | SAM/BAM | BAM datasets and perform other transformations |
| [Samtools ampliconclip](samtools-ampliconclip.md) | SAM/BAM | clip primer bases from bam files |
| [Samtools depth](samtools-depth.md) | SAM/BAM | compute the depth at each position or region |
| [Samtools fastx](samtools-fastx.md) | SAM/BAM | extract FASTA or FASTQ from alignment files |
| [Samtools fixmate](samtools-fixmate.md) | SAM/BAM | fill mate coordinates, ISIZE and mate related flags |
| [Samtools flagstat](samtools-flagstat.md) | SAM/BAM | tabulate descriptive stats for BAM datset |
| [Samtools markdup](samtools-markdup.md) | SAM/BAM | marks duplicate alignments |
| [Samtools merge](samtools-merge.md) | SAM/BAM | merge multiple sorted alignment files |
| [Samtools mpileup](samtools-mpileup.md) | SAM/BAM | multi-way pileup of variants |
| [Samtools sort](samtools-sort.md) | SAM/BAM | order of storing aligned sequences |
| [Samtools view](samtools-view.md) | SAM/BAM | - reformat, filter, or subsample SAM, BAM or CRAM |
| [Calculate sequence complexity](calculate-sequence-complexity.md) | Statistics | total and per read |
| [Count](count.md) | Statistics | occurrences of each record |
| [Perform affine image registration (landmark-based)](perform-affine-image-registration-landmark-based.md) | Statistics |  |
| [Summary Statistics](summary-statistics.md) | Statistics | for any numerical column |
| [rdeval](rdeval.md) | Statistics | Multithreaded read analysis and manipulation tool. |
| [bcftools annotate](bcftools-annotate.md) | VCF/BCF | Annotate and edit VCF/BCF files |
| [bcftools call](bcftools-call.md) | VCF/BCF | SNP/indel variant calling from VCF/BCF |
| [bcftools cnv](bcftools-cnv.md) | VCF/BCF | Call copy number variation from VCF B-allele frequency (BAF) |
| [bcftools csq](bcftools-csq.md) | VCF/BCF | Haplotype aware consequence predictor |
| [bcftools dosage](bcftools-dosage.md) | VCF/BCF | plugin genotype dosage |
| [bcftools filter](bcftools-filter.md) | VCF/BCF | Apply fixed-threshold filters |
| [bcftools query](bcftools-query.md) | VCF/BCF | Extracts fields from VCF/BCF file and prints them in user-de |
| [bcftools stats](bcftools-stats.md) | VCF/BCF | Parses VCF or BCF and produces stats which can be plotted us |
| [bcftools tag2tag](bcftools-tag2tag.md) | VCF/BCF | plugin Convert between similar tags, such as GL and GP |
| [bcftools view](bcftools-view.md) | VCF/BCF | VCF/BCF conversion, view, subset and filter VCF/BCF files |
| [Add LoFreq alignment quality scores](add-lofreq-alignment-quality-scores.md) | Variant Calling | to aligned read SAM/BAM records |
| [BamLeftAlign](bamleftalign.md) | Variant Calling | indels in BAM datasets |
| [Call variants](call-variants.md) | Variant Calling | with LoFreq |
| [DeepVariant](deepvariant.md) | Variant Calling | deep learning-based variant caller |
| [FreeBayes](freebayes.md) | Variant Calling | bayesian genetic variant detector |
| [GATK4 Mutect2](gatk4-mutect2.md) | Variant Calling | - Call somatic SNVs and indels via local assembly of haploty |
| [Insert indel qualities](insert-indel-qualities.md) | Variant Calling | into a BAM file |
| [JasmineSV](jasminesv.md) | Variant Calling | Merge structural variants across samples |
| [SnpEff build:](snpeff-build.md) | Variant Calling | database from Genbank or GFF record |
| [SnpEff chromosome-info:](snpeff-chromosome-info.md) | Variant Calling | list chromosome names/lengths |
| [SnpEff databases:](snpeff-databases.md) | Variant Calling | list available databases |
| [SnpEff download:](snpeff-download.md) | Variant Calling | download a pre-built database |
| [SnpEff eff:](snpeff-eff.md) | Variant Calling | annotate variants |
| [Strelka Germline](strelka-germline.md) | Variant Calling | small variant caller for germline variation in small cohorts |
| [Strelka Somatic](strelka-somatic.md) | Variant Calling | small variant caller for somatic variation in tumor/normal s |
| [bcftools color-chrs](bcftools-color-chrs.md) | Variant Calling | plugin Color shared chromosomal segments, requires phased GT |
| [bcftools frameshifts](bcftools-frameshifts.md) | Variant Calling | plugin Annotate frameshift indels |
| [sniffles](sniffles.md) | Variant Calling | Structural variation caller using third generation sequencin |
| [bamCompare](bamcompare.md) | deepTools | normalizes and compares two BAM files to obtain the ratio, l |
| [plotProfile](plotprofile.md) | deepTools | creates a profile plot for score distributions across genomi |
