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Templates and tools

This page is generated from the app's own catalog (version 2026.17.1), so it always matches what ships: 14 templates and 85 tools.

Templates

A template builds a whole pipeline from your files. The settings that depend on your data (adapter, strandedness, genome size) are asked before the workflow is created.

Template	Field	Level	Reads	Steps	Tools
Genome assembly from long reads (Flye and QUAST) Put long Nanopore or PacBio reads of a microbial genome together without a reference, then measure how good the assembly is.	Genome assembly	Intermediate	Long reads or signal	2	Flye, QUAST
Genome assembly from short reads (SPAdes and QUAST) Put Illumina reads of a microbial genome together without a reference, then measure how good the assembly is.	Genome assembly	Intermediate	Single- or paired-end reads	2	SPAdes, QUAST
ATAC-seq open chromatin peaks with Genrich Find open chromatin regions from paired-end ATAC-seq reads: align, call peaks in ATAC mode, merge them and make a signal track.	Epigenomics	Advanced	Paired-end reads	8	Bowtie2 build, Bowtie2, samtools sort, Genrich, bedtools merge, samtools index, deepTools bamCoverage
Basic read quality check Check the quality of sequencing reads, trim them, check again and get one combined report.	Read quality	Beginner	Single-end reads	4	FastQC, fastp, MultiQC
ChIP-seq peak calling with MACS3 Find where a protein binds the genome: trim, align a ChIP sample and its input control, call peaks, draw the signal and say which genes the peaks lie near.	Epigenomics	Advanced	Single-end reads	14	fastp, Bowtie2 build, Bowtie2, samtools sort, samtools index, MACS3 callpeak, deepTools bamCoverage, deepTools plotFingerprint, HOMER annotatePeaks
Who is in my sample? Kraken2 and Bracken Find which organisms a metagenomic sample contains and how abundant they are: trim, classify the reads with Kraken2, estimate abundances with Bracken and gather the results in one report.	Metagenomics	Intermediate	Single-end reads	4	fastp, Kraken2, Bracken, MultiQC
Nanopore reads from FASTQ to coverage Filter Nanopore reads, check their quality, map them to a genome and measure coverage. Works on every computer.	Long reads	Intermediate	Long reads or signal	6	chopper, NanoPlot, minimap2 (long reads), samtools sort, samtools index, mosdepth
Nanopore from raw signal to coverage Start from the raw POD5 signal files of a Nanopore run: call the bases with Dorado, filter, check the reads, map them to a genome and measure coverage.	Long reads	Advanced	Long reads or signal	10	pod5 merge, pod5 inspect, Dorado basecaller, samtools fastq, chopper, NanoPlot, minimap2 (long reads), samtools sort, samtools index, mosdepth
Ribo-seq with UMIs (riboWaltz) Ribosome profiling with UMIs: trim, extract UMIs, remove rRNA/tRNA/ncRNA, map to transcripts with STAR, deduplicate, riboWaltz report and MultiQC.	RNA sequencing	Advanced	Single-end reads	20	FastQC, Cutadapt, UMI-tools extract, Bowtie2 build, Remove reads matching a database (bowtie2), STAR genome index, STAR (Ribo-seq, transcriptome BAM), samtools view, samtools sort, samtools index, UMI-tools dedup, riboWaltz report, MultiQC
RNA-seq alignment and gene counts Align RNA-seq reads to a genome with HISAT2 and count the reads per gene, ready for differential expression.	RNA sequencing	Intermediate	Single-end reads	7	fastp, HISAT2 build, HISAT2, samtools sort, samtools index, featureCounts, MultiQC
RNA-seq quantification with Salmon Estimate how much of each transcript is present in an RNA-seq sample, without aligning the reads to a genome.	RNA sequencing	Intermediate	Single-end reads	4	fastp, Salmon index, Salmon quant, MultiQC
Germline variant calling, paired-end reads (bcftools) Find variants in one paired-end sample against a reference genome, with alignment statistics and a filtered VCF.	DNA sequencing	Intermediate	Paired-end reads	10	BWA index, BWA MEM, samtools sort, samtools markdup, samtools index, samtools flagstat, bcftools call, bcftools filter, bcftools stats, MultiQC
Germline variant calling with bcftools Find single-base differences between one sample and a reference genome, from trimming to a filtered, summarised VCF.	DNA sequencing	Intermediate	Single-end reads	10	fastp, BWA index, BWA MEM, samtools sort, samtools markdup, samtools index, bcftools call, bcftools filter, bcftools stats, MultiQC
Germline variant calling with GATK Find variants in one sample with GATK HaplotypeCaller, the standard caller for human and other diploid genomes.	DNA sequencing	Advanced	Single-end reads	11	fastp, BWA index, BWA MEM, samtools sort, Picard MarkDuplicates, samtools index, samtools faidx, GATK CreateSequenceDictionary, GATK HaplotypeCaller, bcftools stats, MultiQC

Catalog tools

Each entry names every file it reads and writes, installs the tool at a pinned version and was run against the real program. Jump to: Quality control | Trimming | Reference preparation | Alignment | BAM processing | Variant calling | Variant annotation | Quantification | Peak calling and epigenomics | Signal tracks and plots | Genome intervals | FASTA and FASTQ tools | Assembly | Metagenomics | Nanopore signal data

Quality control 9

Tool	What it does	Reads	Makes	Installed as
FastQC Read quality	Quality report for raw sequencing reads.	fastq	html, zip	fastqc 0.13.0 (bioconda)
MultiQC Report summaries	Combines the reports of many tools into one HTML page.	any	html	multiqc 1.35 (bioconda)
mosdepth Coverage	Fast coverage summary: the average depth per chromosome and in windows along the genome.	bam, bai	txt, bed	mosdepth 0.3.13 (bioconda)
Qualimap BamQC Alignment QC	Quality report of an alignment: coverage, mapping quality, insert size and base content.	bam	html, txt	qualimap 2.3 (bioconda)
RSeQC infer experiment RNA-seq QC	Works out whether an RNA-seq library is stranded, and which way, from where reads fall on genes.	bam, bed	txt	rseqc 5.0.5 (bioconda)
RSeQC read distribution RNA-seq QC	Shows how the reads divide between exons, introns and the regions around genes.	bam, bed	txt	rseqc 5.0.5 (bioconda)
deepTools plotFingerprint Enrichment	Shows how well a ChIP-seq or ATAC-seq sample is enriched: a good ChIP puts most of its reads into a small part of the genome, an input control spreads them evenly.	bam, bai	image, tsv	deeptools 3.5.6 (bioconda)
NanoPlot Long-read QC	Summarises a Nanopore or PacBio run: how many reads, how long and how accurate, with plots. Reads FASTQ, a Dorado BAM or a sequencing summary.	fastq, fasta, bam, tsv	html, txt	nanoplot 1.48.0 (bioconda)
seqkit stats Sequence statistics	Counts the sequences in FASTA or FASTQ files and reports their total length, shortest, longest, N50 and average quality, one line per file.	fastq, fasta	tsv	seqkit 2.14.0 (bioconda)

Trimming 6

Tool	What it does	Reads	Makes	Installed as
fastp Trim and filter reads	Fast adapter and quality trimming for FASTQ reads.	fastq	fastq, html, json	fastp 1.3.7 (bioconda)
Cutadapt Trim and filter reads	Removes adapter sequences and low-quality ends from reads.	fastq	fastq, txt	cutadapt 5.2 (bioconda)
Filtlong Long-read filtering	Keeps the best long reads of a Nanopore or PacBio run: drops reads that are too short or too inaccurate, and can keep only as many bases as you need. Writes a compressed FASTQ.	fastq	fastq	filtlong 0.3.1 (bioconda)
chopper Long-read filtering	Filters and trims long reads by their average quality and length. Fast, and the usual first step for Nanopore reads. Writes a compressed FASTQ.	fastq	fastq	chopper 0.14.1 (bioconda)
UMI-tools extract UMI handling	Moves each read's UMI (unique molecular identifier) into its name and cuts it, and any spacer next to it, out of the sequence. Run it before aligning so duplicates can be removed later.	fastq	fastq, txt	umi_tools 1.1.6 (bioconda)
Remove reads matching a database (bowtie2) Remove contaminant reads	Aligns reads to sequences you do not want (rRNA, tRNA, small RNAs, PhiX, a contaminant genome) and keeps the reads that do not match. Matches are counted in the log, not saved.	index, fastq	fastq, txt	bowtie2 2.5.5 (bioconda)

Reference preparation 10

Tool	What it does	Reads	Makes	Installed as
BWA index Aligner indexes	Builds the index BWA MEM needs to align reads to a genome.	fasta	index, fasta	bwa 0.7.19 (bioconda)
Bowtie2 build Aligner indexes	Builds the genome index Bowtie2 needs to align reads.	fasta	index	bowtie2 2.5.5 (bioconda)
samtools faidx Reference indexes	Indexes a reference FASTA (makes the .fai file variant callers need).	fasta	fasta, fai	samtools 1.24 (bioconda)
GATK CreateSequenceDictionary Reference indexes	Makes the sequence dictionary (.dict) that GATK needs next to the reference.	fasta	fasta, fai, dict	gatk4 4.6.2.0 (bioconda)
HISAT2 build Aligner indexes	Builds the genome index HISAT2 needs to align RNA-seq reads.	fasta	index	hisat2 2.2.3 (bioconda)
Salmon index Aligner indexes	Builds the index Salmon quant needs from transcript sequences.	fasta	index	salmon 2.8.0 (bioconda)
STAR genome index Aligner indexes	Builds the genome index STAR needs to align RNA-seq reads, with the known splice junctions of an annotation.	fasta, gtf	index	star 2.7.10b (bioconda)
kallisto index Aligner indexes	Builds the index kallisto quant needs from transcript sequences.	fasta	index	kallisto 0.52.0 (bioconda)
gffread transcripts Annotation files	Cuts the transcript sequences (exons joined together) out of a genome using an annotation.	fasta, gtf	fasta	gffread 0.12.9 (bioconda)
Annotation to BED12 Annotation files	Converts a gene annotation (GTF or GFF3) to the BED12 gene model that RSeQC reads.	gtf	bed	gffread 0.12.9 (bioconda)

Alignment 7

Tool	What it does	Reads	Makes	Installed as
BWA MEM DNA aligners	Aligns reads to a reference genome. Writes SAM.	fasta, fastq	sam	bwa 0.7.19 (bioconda)
Bowtie2 DNA aligners	Aligns reads to an indexed genome, single-end or as read pairs. Writes SAM.	index, fastq	sam	bowtie2 2.5.5 (bioconda)
minimap2 (short reads) DNA aligners	Aligns short reads (the sr preset) to a reference genome. Writes SAM with a read group.	fasta, fastq	sam	minimap2 2.30 (bioconda)
STAR RNA-seq aligners	Splice-aware RNA-seq aligner, single-end or paired-end. Writes a coordinate-sorted BAM.	index, fastq	bam, txt	star 2.7.10b (bioconda)
HISAT2 RNA-seq aligners	Splice-aware RNA-seq aligner, single-end or paired-end. Writes SAM.	index, fastq	sam, txt	hisat2 2.2.3 (bioconda)
minimap2 (long reads) Long-read aligners	Aligns long reads (Nanopore, PacBio HiFi or cDNA) to a reference genome. Pick the preset that matches how the reads were made. Writes SAM.	fasta, fastq	sam	minimap2 2.30 (bioconda)
STAR (Ribo-seq, transcriptome BAM) RNA-seq aligners	Aligns footprint reads to the genome and writes them in transcript coordinates, as riboWaltz needs. Defaults suit short footprints; reads that did not align stay in the BAM, marked unmapped.	index, fastq	bam, txt	star 2.7.10b (bioconda)

BAM processing 10

Tool	What it does	Reads	Makes	Installed as
samtools sort Alignment files	Sorts alignments by coordinate (or by read name).	sam, bam	bam	samtools 1.24 (bioconda)
samtools index Alignment files	Builds the .bai index of a coordinate-sorted BAM.	bam	bai	samtools 1.24 (bioconda)
samtools view Alignment files	Filters alignments and converts them to BAM.	sam, bam	bam	samtools 1.24 (bioconda)
samtools flagstat Alignment files	Counts reads by alignment flag. Writes a text summary.	sam, bam	txt	samtools 1.24 (bioconda)
samtools fastq Alignment files	Turns an unaligned BAM, such as the output of the Dorado basecaller, into a FASTQ file of reads. Writes compressed FASTQ.	bam	fastq	samtools 1.24 (bioconda)
samtools merge Alignment files	Combines several sorted BAM files into one.	bam	bam	samtools 1.24 (bioconda)
samtools markdup Duplicates	Finds PCR duplicates and marks (or removes) them. Runs fixmate and sort first, so plain aligner output works.	sam, bam	bam, txt	samtools 1.24 (bioconda)
Picard MarkDuplicates Duplicates	Finds PCR duplicates in a sorted BAM and marks (or removes) them. Writes a duplication report.	bam	bam, txt	picard 3.4.0 (bioconda)
samtools depth Coverage	Writes how many reads cover each position of the genome, one column per BAM file.	bam	tsv	samtools 1.24 (bioconda)
UMI-tools dedup Duplicates	Removes PCR duplicates: reads with the same start and UMI (allowing for UMI errors) count once. Needs a sorted BAM with its index, and read names that end in the UMI.	bam, bai	bam, txt	umi_tools 1.1.6 (bioconda)

Variant calling 8

Tool	What it does	Reads	Makes	Installed as
bcftools call SNPs and small indels	Calls SNPs and indels from a sorted BAM (mpileup then call).	fasta, bam	vcf	bcftools 1.24 (bioconda)
FreeBayes SNPs and small indels	Calls SNPs and small indels from one or more sorted, indexed BAM files.	fasta, bam	vcf	freebayes 1.3.10 (bioconda)
GATK HaplotypeCaller SNPs and small indels	Calls SNPs and small indels by re-assembling the reads around each variant.	fasta, bam, bai	vcf	gatk4 4.6.2.0 (bioconda)
bcftools filter VCF tools	Keeps the variants that are good enough (enough quality and depth), or marks the others.	vcf	vcf	bcftools 1.24 (bioconda)
bcftools norm VCF tools	Writes variants in one standard form: indels left-aligned, optionally one line per alternative allele.	vcf, fasta	vcf	bcftools 1.24 (bioconda)
bcftools stats VCF tools	Counts the variants in a VCF: SNPs, indels, transitions and transversions. MultiQC reads it.	vcf	txt	bcftools 1.24 (bioconda)
bgzip VCF tools	Compresses a VCF, BED or other table so it can be indexed with tabix.	vcf, bed, gtf, tsv	vcf, bed, gtf, tsv	htslib 1.24 (bioconda)
tabix VCF tools	Indexes a compressed, sorted VCF, BED or GFF so a region can be read without reading the whole file.	vcf, bed, gtf, tsv	vcf, bed, gtf, tsv, tbi	htslib 1.24 (bioconda)

Variant annotation 2

Tool	What it does	Reads	Makes	Installed as
snpEff build database Custom databases	Builds a snpEff database for your own genome from its FASTA and gene annotation (GTF).	fasta, gtf	database	snpeff 5.4.0c (bioconda)
snpEff annotate Variant effects	Says what each variant does to the genes: missense, synonymous, intron, intergenic and so on. Needs a snpEff database.	vcf, database	vcf, html, tsv	snpeff 5.4.0c (bioconda)

Quantification 5

Tool	What it does	Reads	Makes	Installed as
Salmon quant Transcript abundance	Quantifies transcript abundance from single-end reads.	index, fastq	tsv	salmon 2.8.0 (bioconda)
featureCounts Gene counts	Counts reads per gene from alignments and an annotation.	bam, sam, gtf	tsv, txt	subread 2.1.1 (bioconda)
kallisto quant Transcript abundance	Quantifies transcript abundance from single-end or paired-end reads, without aligning them.	index, fastq	tsv, txt	kallisto 0.52.0 (bioconda)
StringTie assemble Transcript assembly	Assembles transcripts from RNA-seq alignments, optionally guided by a gene annotation, and estimates their abundance.	bam, gtf	gtf, tsv	stringtie 3.0.3 (bioconda)
StringTie quantify Transcript assembly	Measures the abundance of the transcripts of an annotation (no new transcripts are made).	bam, gtf	gtf, tsv	stringtie 3.0.3 (bioconda)

Peak calling and epigenomics 3

Tool	What it does	Reads	Makes	Installed as
MACS3 callpeak Peak calling	Finds the places in the genome where a ChIP-seq (or ATAC-seq) sample has more reads than expected, with an optional input control. Makes sharp peaks, summits and a signal track.	bam	peaks, bed, tsv, bedgraph	macs3 3.0.5 (bioconda)
Genrich Peak calling	Finds open chromatin in ATAC-seq data (or enriched regions in ChIP-seq). It reads all replicates together and takes the Tn5 cut sites into account.	bam, bed	peaks, bed	genrich 0.6.1 (bioconda)
HOMER annotatePeaks Peak annotation	Tells you where each peak lies: in a promoter, an exon, an intron or between genes, and which gene is closest. Uses the genome FASTA and gene annotation you connect. Needs a Genome FASTA and gene annotation.	bed, peaks, fasta, gtf	tsv, txt	homer 5.1 (bioconda)

Signal tracks and plots 4

Tool	What it does	Reads	Makes	Installed as
deepTools bamCoverage Signal tracks	Turns alignments into a signal track (bigWig) that shows how many reads cover each stretch of the genome, scaled so that samples can be compared.	bam, bai, bed	bigwig	deeptools 3.5.6 (bioconda)
deepTools computeMatrix Signal around regions	Collects the signal around one point of every region (the centre of each peak, or the start of each gene) into a table. plotHeatmap draws it.	bigwig, bed, peaks, gtf	matrix, bed, tsv	deeptools 3.5.6 (bioconda)
deepTools plotHeatmap Plots	Draws a heatmap of the signal around your regions, one row per region, with an average profile on top.	matrix	image	deeptools 3.5.6 (bioconda)
riboWaltz report Ribosome profiling	Finds where the ribosome sits in each footprint (the P-site offset) and writes one HTML report: lengths, offsets, 3-nt periodicity, start and stop profiles, regions, codon usage, plus TSV tables.	bam, gtf, fasta	html, tsv	ribowaltz 2.0 (bioconda)

Genome intervals 4

Tool	What it does	Reads	Makes	Installed as
bedtools intersect Compare regions	Compares two sets of regions: keeps the ones that overlap, the ones that do not, or just the overlapping stretches. For example, which peaks of one sample are also peaks in another.	bed, peaks, gtf, vcf	bed, peaks	bedtools 2.31.1 (bioconda)
bedtools merge Combine regions	Joins regions that overlap (or lie close together) into single regions. Give it the peaks of several samples to get one combined set.	bed, peaks	bed	bedtools 2.31.1 (bioconda)
bedtools genomecov Coverage	Measures how deeply every stretch of the genome is covered by reads and writes it as a bedGraph track.	bam	bedgraph	bedtools 2.31.1 (bioconda)
bedtools getfasta Sequences	Cuts the DNA sequence of every region out of a genome FASTA, for example the sequences under your peaks for a motif search.	fasta, bed, peaks, gtf	fasta	bedtools 2.31.1 (bioconda)

FASTA and FASTQ tools 2

Tool	What it does	Reads	Makes	Installed as
seqkit seq (filter or convert) Filter and convert	Keeps the sequences within a length or quality range, and can reverse-complement or upper-case them. Writes a compressed file.	fastq, fasta	fastq, fasta	seqkit 2.14.0 (bioconda)
seqkit grep (pick sequences) Pick sequences	Picks sequences by name or by a stretch of sequence, from a list of names or a pattern you type. Can also leave those out instead.	fastq, fasta, txt, tsv	fastq, fasta	seqkit 2.14.0 (bioconda)

Assembly 3

Tool	What it does	Reads	Makes	Installed as
Flye Long-read assemblers	Assembles a genome from long reads (Nanopore or PacBio) without a reference. Writes the contigs, the assembly graph and a table of contig lengths and coverage.	fastq, fasta	fasta, gfa, tsv, txt	flye 2.9.6 (bioconda)
SPAdes Short-read assemblers	Assembles a genome from short Illumina reads without a reference. Writes the contigs, the scaffolds and the assembly graph.	fastq	fasta, gfa, txt	spades 4.2.0 (bioconda)
QUAST Assembly quality	Judges genome assemblies: how many contigs, how long, and (with a reference) how complete and correct. Several assemblies go into one comparison.	fasta	tsv, html, txt	quast 5.3.0 (bioconda)

Metagenomics 4

Tool	What it does	Reads	Makes	Installed as
Kraken2 build database Databases	Builds a Kraken2 database from your own genomes, for example the few species you expect in a sample. Needs a taxonomy that names every genome.	fasta, taxonomy	database	kraken2 2.17.1 (bioconda)
Kraken2 Classification	Names the organism each read most likely comes from (its taxonomy) by matching it against a database of genomes. Writes a summary table by species and a line for every read. Needs a Kraken2 database.	fastq, fasta, database	tsv, txt	kraken2 2.17.1 (bioconda)
Bracken prepare database Databases	Gets a Kraken2 database ready for Bracken. Makes a new folder that links to your database and adds the files Bracken needs for one read length. Your database is not changed. Needs a Kraken2 database.	database	database	bracken 2.6.1 (bioconda)
Bracken Abundance	Turns a Kraken2 summary into better abundance estimates. Reads that Kraken2 could only place on a genus are shared out over the species of that genus. Needs a Bracken database.	tsv, txt, database	tsv, txt	bracken 2.6.1 (bioconda)

Nanopore signal data 8

Tool	What it does	Reads	Makes	Installed as
pod5 view POD5 files	Lists the reads in POD5 files as a table: read ID, channel, length in samples, start time and more. Use it to pick reads for pod5 filter or pod5 subset.	pod5	tsv	pod5 0.3.48 (bioconda)
pod5 inspect POD5 files	Reports what a POD5 file holds: how many reads it has, how they are grouped into batches, and the version of the file format.	pod5	txt	pod5 0.3.48 (bioconda)
pod5 filter POD5 files	Copies only the reads you list into a new POD5 file. Use it to basecall or share a small part of a run.	pod5, txt, tsv	pod5	pod5 0.3.48 (bioconda)
pod5 subset (split by column) POD5 files	Splits POD5 files into several files by a value in a table, for example one file per channel. The table can come from pod5 view or from a sequencing summary.	pod5, tsv	pod5	pod5 0.3.48 (bioconda)
pod5 merge POD5 files	Joins several POD5 files into one, for example the many files MinKNOW writes during a run.	pod5	pod5	pod5 0.3.48 (bioconda)
pod5 convert from FAST5 POD5 files	Converts old FAST5 signal files to one POD5 file, the format Dorado reads.	fast5	pod5	pod5 0.3.48 (bioconda)
Dorado basecaller Basecalling	Turns the raw signal of a Nanopore run (POD5) into DNA sequence. Writes an unaligned BAM. Needs a graphics card or an Apple chip for anything but tests. Needs a Basecalling model.	pod5	bam	dorado 1.4.0 (downloaded from the vendor, Oxford Nanopore Technologies Public License)
Dorado summary Basecalling	Makes a table with one line per read from a Dorado BAM: read ID, channel, length and quality. NanoPlot and pod5 subset read it.	bam	tsv	dorado 1.4.0 (downloaded from the vendor, Oxford Nanopore Technologies Public License)