Supported Tools

Removes adapter sequences, trims low quality bases from 3' ends, or merges overlapping pairs into consensus

Automatic filtering, trimming, error removing, and quality control for FastQ data

Quality controls Illumina libraries sequenced on Oxford Nanopore flowcells

Rapid & standardized annotation of bacterial genomes, MAGs & plasmids

Lightweight tool to stat the depth coverage of target regions of BAM file(s)

Provides both a programmer's API and an end-user's toolkit for handling BAM files

Common data-quality-related trimming, filtering, and masking operations with a kmer based approach

Pre-processing, assembly, alignment, and statistics tools for DNA/RNA sequencing reads

Utilities for variant calling and manipulating VCFs and BCFs

Demultiplexes data and converts BCL files to FASTQ file formats for downstream analysis

Demultiplexes data and converts BCL files to FASTQ file formats for downstream analysis

Tools for early stage alignment file processing

Assigns reads to different references using bloom filters. This is faster than alignment and can be used for contamination detection

Maps bisulfite converted DNA sequence reads and determines cytosine methylation states

Maps bisulfite converted sequence reads and determine cytosine methylation states

Ultrafast, memory-efficient short read aligner

Results from both Bowtie 2 and HISAT2, tools for aligning reads against a reference genome

Computes the abundance of species in DNA sequences from a metagenomics sample

Assesses genome assembly and annotation completeness

Tools for BUS files - a file format for single-cell RNA-seq data designed to facilitate the development of modular workflows for data processing

PacBio tool that generates highly accurate single-molecule consensus reads (HiFi Reads)

Analyzes single cell expression or VDJ data produced by 10X Genomics

Checks a set of quality criteria against an Illumina runfolder

Adapter clipping and read merging for ancient DNA data

Simple and flexible bioinformatics pipeline tool

Estimates concordance and contamination for tumor–normal pairs

Finds and removes adapter sequences, primers, poly-A tails, and other types of unwanted sequences

DNA damage pattern retrieval for ancient DNA analysis

Improved Duplicate Removal for merged/collapsed reads in ancient DNA analysis

Tools to process and analyze deep sequencing data

Sequence aligner for protein and translated DNA searches, a drop-in replacement for the NCBI BLAST

Disambiguate reads aligned to two different species (e.g. human and mouse)

Illumina Bio-IT Platform that uses FPGA for secondary analysis of sequencing data

Illumina Bio-IT Platform that uses FPGA for secondary analysis of sequencing data

Tools to compare and manipulate the contents of EingenStrat databases, and to calculate SNP coverage statistics in such databases

All-in-one FASTQ preprocessor (QC, adapters, trimming, filtering, splitting...)

Screens a library of sequences in FastQ format against a set of sequence databases to see if the composition of the library matches with what you expect

Quality control tool for high throughput sequencing data

Counts mapped reads for genomic features such as genes, exons, promoter, gene bodies, genomic bins and chromosomal locations

Processing and evaluating data containing UMIs

Filters long reads by quality

Merges paired-end reads from next-generation sequencing experiments

Barcode and adapter removal tool

Recovers relative lineage abundances from mixed SARS-CoV-2 samples

Metagenomics classification: quickly assigns sequence fragments to their closest reference among thousands of references via Interleaved Bloom Filters of k-mer/minimizers

Wide variety of tools with a primary focus on variant discovery and genotyping

Tool to compare, merge and annotate one or more GFF files with a reference annotation in GFF format

Low-coverage whole genome sequencing imputation

Quickly estimate coverage from a whole-genome bam index, providing 16KB resolution

Calls peaks in CUT&TAG/CUT&RUN datasets

Benchmarks variant calls against gold standard truth datasets

Hi-C analysis from processing to visualization

Pipeline for Hi-C data processing

Mapping and quality control on Hi-C data

Haplotype-resolved assembler for accurate Hifi reads

Maps DNA or RNA reads against a genome or a population of genomes

Motif discovery and next-gen sequencing analysis

Ancient DNA characteristics screening tool of output from the metagenomic aligner MALT

Removes host sequences from short and long read (meta)genomes, from paired or unpaired fastq[.gz]

Part of the HTSeq package: counts reads covering specified genomic features

Reference-free tool to quickly remove duplicates from FastQ files, with or without UMIs

Reading and writing InterOp metric files

Identifies transcripts in PacBio single-molecule sequencing data (HiFi reads)

Functions for viral amplicon-based sequencing

Computes statistics on genome annotation

Counting k-mers in DNA

Taxonomic classification for metagenomics

Quantifies abundances of transcripts (or more generally, of target sequences) from RNA-Seq data

Analyses sequencing data via its k-mer spectra

Taxonomic classification tool that uses exact k-mer matches to find the lowest common ancestor (LCA) of a given sequence

Bayesian reconstruction of ancient DNA

Predicts the sequencing library type from the base composition of a FastQ file

Demultiplex PacBio single-molecule sequencing reads

Sample demultiplexing, barcode processing, alignment, quality control, variant calling, phasing, and structural variant calling

Identifies transcription factor binding sites in ChIP-seq data

Aligns of metagenomic reads to a database of reference sequences (such as NR, GenBank or Silva) and outputs a MEGAN RMA file

Tracks and quantifies damage patterns in ancient DNA sequences

NGS read assembler

Profiles the composition of microbial communities from metagenomic shotgun sequencing data

Methylation sequencing data quality assessment tool

Quality control for ONT (Oxford Nanopore) long reads

Annotates miRNAs and isomiRs and compute general statistics in mirGFF3 format

Quality control for small RNA sequencing data

Fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing

Microbial profiling through marker gene (MG)-based operational taxonomic units (mOTUs)

Computes mitochondrial to nuclear genome ratios in NGS datasets

Reads multiple VCF files into combined genotype calls, produces summary statistics and downstream formats

Reports read quality and length from nanopore sequencing data

Reports various statistics for long read dataset in FASTQ, BAM, or albacore sequencing summary format (supports NanoPack; NanoPlot, NanoComp)

Viral genome alignment, clade assignment, mutation calling, and quality checks

Calculating statistics from FASTQ, BAM, and VCF

Forensic tool for by backwards computing library information in sequencing data

Estimates metagenomic coverage and sequence diversity

Analysis and manipulation of pangenome graphs structured in the variation graph model

Precision HLA typing from next-generation sequencing data

Toolkit for Chromatin Conformation Capture experiments. Handles short-reads paired reference alignments, extracts 3C-specific information, and perform common tasks such as sorting, filtering, and deduplication

Uses variant calls to assign SARS-CoV-2 genome sequences to global lineages

Takes one or multiple sequencing chips of an amplified libray as HiFi reads and marks or removes duplicates

Compares familial-relationships and sexes as reported in a PED file with those inferred from a VCF

Computes informative enrichment and quality measures for ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data

Tools for manipulating high-throughput sequencing data

Finds and removes adapters from Oxford Nanopore reads

Estimates library complexity, showing how many additional unique reads are sequenced for increasing total read count

C++ implementation of the prinseq-lite.pl program. Filters, reformats, and trims genomic and metagenomic reads

Rapid annotation of prokaryotic genomes

A purity, ploidy and copy number estimator for whole genome tumor data

Identifies, orients, trims and rescues full length Nanopore cDNA reads. Can also rescue fused reads

Computes metrics and generates interactive QC plots for Oxford Nanopore technologies sequencing data

Reference-free and BAM based quality control for Hi-C data

Toolkit for analysis, QC, and data management of RNA-Seq datasets

Quality control of alignment data and its derivatives like feature counts

Quality assessment tool for genome assemblies

RNA-Seq metrics for quality control and process optimization

Bacterial RNA-seq analysis: align reads to coding sequences, rRNAs, tRNAs, and miscellaneous RNAs

Estimates gene and isoform expression levels from RNA-Seq data

Evaluates high throughput RNA-seq data

Quantifies expression of transcripts using RNA-seq data

Toolkit for interacting with BAM/CRAM files

Marks duplicates and extracts discordant and split reads from sam files

Toolkit for interacting with BAM/CRAM files

Separates mixed-species RNA-seq reads according to their species of origin

Reports statistics generated by the Seqera Platform CLI

Sequencing quality control for both long-read and short-read data

Determines FASTQ(A) sequencing file source protocol and the species of origin, to check that the composition of the library is expected

Filters adapters, vectors, and contaminants while quality trimming

Calculates relative coverage of X and Y chromosomes and their associated error bars from the depth of coverage at specified SNPs

A windowed adaptive trimming tool for FASTQ files using quality

Adapter trimming tool for NGS paired-end sequences

Tool to analyze SLAM-Seq data

Rapid haploid variant calling and core genome alignment

Annotates and predicts the effects of variants on genes (such as amino acid changes)

Allele-specific alignment sorter. Determines allelic origin of reads that cover known SNP positions

Genotype to pedigree correspondence checks from sketches derived from BAM/CRAM or VCF

Program for filtering, mapping and OTU-picking NGS reads in metatranscriptomic and metagenomic data

Quickly searches, compares, and analyzes genomic and metagenomic data sets

Tool to analyze 10x Genomics spatial transcriptomics data

Analyzes restriction enzyme-based data (e.g. RAD-seq)

Universal RNA-seq aligner

De novo genome assembler of 10X Genomics linked-reads

Estimates tumour purity and clonal / subclonal copy number

Splice junction RNA-Seq reads mapper for mammalian-sized genomes

Read trimming tool for Illumina NGS data

Benchmarking, merging, and annotating structural variants

Tools for dealing with Unique Molecular Identifiers (UMIs)/(RMTs) and scRNA-Seq barcodes

Variant detection in massively parallel sequencing data

Program to analyse and reporting on VCF files

Determines the effect of variants on genes, transcripts and protein sequences, as well as regulatory regions

Detects sample contamination and/or sample swaps

Toolkit to manipulate and analyze graphical genomes, including read alignment

Phasing genomic variants using DNA reads (aka read-based phasing, or haplotype assembly)

Fast xenograft read sorter based on space-efficient k-mer hashing

Classifies reads from xenograft sources