Software

An integrated tool for Structural Variations annotation and ranking

used to functionally annotate genetic variants detected from diverse genomes

Sequence annotation tool

Bakta is a tool for the rapid & standardized annotation of bacterial genomes and plasmids from both isolates and MAGs.

Gene annotation tool

DFAST-core is the stand-alone version of DFAST, a flexible and customizable pipeline for prokaryotic genome annotation as well as data submission to the INSDC

DRAM (Distilled and Refined Annotation of Metabolism) is a tool for annotating metagenomic assembled genomes and VirSorter identified viral contigs.

tool for fast functional annotation of novel sequences

Helixer is a tool for structural genome annotation. It utilizes Deep Neural Networks and a Hidden Markov Model to directly provide primary gene models in a gff3 file.

Anotación de proteinas

Genome annotation software

Fills the bioinformatics needs of the microbial ecology community

fast, accurate and comprehensive platform for comparative genomics. It finds orthogroups and orthologs

Tool for annotating bacteries.

Takes annotated assemblies in GFF3 format and calculates the pan genome.

Sma3 annotation software

Genetic variant annotation and effect prediction toolbox

TElocal takes RNA-seq (and similar data) and annotates reads to both genes & transposable elements.

Trinotate is a comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms.

Variant effect Predictor

Control-FREEC is a tool for detection of copy-number changes and allelic imbalances (including LOH) using deep-sequencing data

Discovers active known or novel miRNAs from deep sequencing data.

ProteoWizard provides a set of open-source, cross-platform software libraries and tools (e.g. msconvert, Skyline, IDPicker, SeeMS) that facilitate proteomics data analysis.

sRNAtoolbox is a collection of several tools for RNA based research, including expression profiling from NGS data, differential expression, analysis of unmapped reads with blast and consensus target prediction and analysis.

Genome-wide copy number from targeted DNA sequencing

Deepvariant is a deep learning-based variant caller

Bayesian haplotype-based polymorphism discovery and genotyping

The toolkit offers a wide variety of tools, with a primary focus on variant discovery and genotyping as well as strong emphasis on data quality assurance

A probabilistic framework for structural variant discovery.

Plink is a whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.

RepEnrich is a method to estimate repetitive element enrichment using high-throughput sequencing data.

Strelka2 germline and somatic small variant caller

VarScan is a platform-independent mutation caller for targeted, exome, and whole-genome resequencing data generated on Illumina, SOLiD, Life/PGM, Roche/454, and similar instruments.

A simple C++ library for parsing and manipulating VCF files, + many command-line utilities

collection of tools and class interfaces for the assembly of DNA reads

assessing genome assembly and annotation completeness with single-copy orthologs

BWA is a software package for mapping low-divergent sequences against a large reference genome

Canu specializes in assembling PacBio or Oxford Nanopore sequences

Accurate assembly of minority viral haplotypes from next-generation sequencing through efficient noise reduction.

Hifiasm is a fast haplotype-resolved de novo assembler for PacBio HiFi reads

HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis. It is a collection of command line programs for UNIX-style operating systems written in Perl and C++. HOMER was primarily written as a de novo motif discovery algorithm and is well suited for finding 8-20 bp motifs in large scale genomics data. HOMER contains many useful tools for analyzing ChIP-Seq, GRO-Seq, RNA-Seq, DNase-Seq, Hi-C and numerous other types of functional genomics sequencing data sets.

KmerGenie estimates the best k-mer length for genome de novo assembly. Given a set of reads, KmerGenie first computes the k-mer abundance histogram for many values of k. Then, for each value of k, it predicts the number of distinct genomic k-mers in the dataset, and returns the k-mer length which maximizes this number.

Cabog assembler modified for pine

MEGAHIT is an ultra-fast and memory-efficient NGS assembler

Metassembler combines multiple whole genome de novo assemblies into a combined consensus assembly using the best segments of the individual assemblies

A versatile pairwise aligner for genomic and spliced nucleotide sequences

a system for rapidly aligning entire genomes

Fast and accurate de novo assembler for long reads

QUAST evaluates genome assemblies. QUAST works both with and without a reference genome. The tool accepts multiple assemblies, thus is suitable for comparison.

RagTag is a collection of software tools for scaffolding and improving modern genome assemblies

Genome assembly

A de novo transcriptome assembler designed specifically for RNA-Seq

SPAdes is a single-cell genome assembler

Stringtie is an assembler of RNA-Seq alignments into potential transcripts.

Aligns RNA-Seq reads to a genome in order to identify exon-exon splice junctions

Assembler for DNA/RNA sequences

hybrid genome assembly pipeline developed for telomere-to-telomere assembly of PacBio HiFi and Oxford Nanopore reads

//github.com/NBISweden/AGAT

AMRFinderPlus - Identify AMR genes and point mutations, and virulence and stress resistance genes in assembled bacterial nucleotide and protein sequence.

AntiSMASH identifies Biosynthetic Gene Clusters (BGCs) of bacteria and fungi encoding secondary metabolites of all known broad chemical classes, based on hidden Markov models.

AUGUSTUS predicts genes in eukaryotic genomic sequences

Bactopia is a flexible pipeline for complete analysis of bacterial genomes

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

Utilidades para procesar ficheros BAM

Barrnap predicts the location of ribosomal RNA genes in genomes. It supports bacteria (5S,23S,16S), archaea (5S,5.8S,23S,16S), metazoan mitochondria (12S,16S) and eukaryotes (5S,5.8S,28S,18S).

Converts from Illumina format, BCL, to Fastq

the fast, highly scalable and easily-parallelizable genome analysis toolkit

swiss-army knife of tools for a wide-range of genomics analysis

BiG-SCAPE (Biosynthetic Gene Similarity Clustering and Prospecting Engine) is a software package, written in Python, that constructs sequence similarity networks of Biosynthetic Gene Clusters (BGCs) and groups them into Gene Cluster Families (GCFs).

Bracken is a companion program to Kraken 1, KrakenUniq, or Kraken 2 While Kraken classifies reads to multiple levels in the taxonomic tree, Bracken allows estimation of abundance at a single level using those classifications (e.g. Bracken can estimate abundance of species within a sample).

BigWig visualizer tool

microbial classification engine

CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes

Rapid assessment of genome bin quality using machine learning.

CheckV is a fully automated command-line pipeline for assessing the quality of single-contig viral genomes, including identification of host contamination for integrated proviruses, estimating completeness for genome fragments, and identification of closed genomes.

comprehensive and integrative circular RNA analysis toolset.

CIRIquant is a comprehensive analysis pipeline for circRNA detection and quantification in RNA-Seq data

a tool set for pathway based data integration and visualization

Effective binning of metagenomic contigs using COntrastive Multi-viEw representation learning

enables the easy detection of CRISPRs and cas genes

Detect CRISPR-Cas genes and arrays, and predict the subtype based on both Cas genes and CRISPR repeat sequence.

The dada2 package infers exact amplicon sequence variants (ASVs) from high-throughput amplicon sequencing data, replacing the coarser and less accurate OTU clustering approach. The dada2 pipeline takes as input demultiplexed fastq files, and outputs the sequence variants and their sample-wise abundances after removing substitution and chimera errors. Taxonomic classification is available via a native implementation of the RDP naive Bayesian classifier, and species-level assignment to 16S rRNA gene fragments by exact matching.

deepSRAMP is the sucessor of the popular mammalian m6A site predictor SRAMP. It greatly outperforms its predecessor.

Oxford Nanopore's Basecaller.

Tool for converting file type

Fast, parallel, highly accurate Maximum Likelihood Phylogenetic Placement, by the team behind RAxML(-ng)

A Python framework for the analysis and visualization of trees.

ExOrthist is a Nextflow based pipeline to infer exon orthology groups at all evolutionary distances.

There are a number of regions in the human genome consisting of repetitions of short unit sequence (commonly a trimer). Expansion Hunter aims to estimate sizes of such repeats by performing a targeted search through a BAM/CRAM file for reads that span, flank, and are fully contained in each repeat

FastANI is developed for fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI)

flDPnn Predictor

Fast genome analysis from unassembled short reads

The GenomeTools (gt) genome analysis system

Genrich is a peak-caller for genomic enrichment assays (e.g. ChIP-seq, ATAC-seq). It analyzes alignment files generated following the assay and produces a file detailing peaks of significant enrichment.

compare and evaluate the accuracy of RNA-Seq transcript assemblers

//github.com/gpertea/gffcompare

GRIDSS is a module software suite containing tools useful for the detection of genomic rearrangements. GRIDSS includes a genome-wide break-end assembler, as well as a structural variation caller for Illumina sequencing data. GRIDSS calls variants based on alignment-guided positional de Bruijn graph genome-wide break-end assembly, split read, and read pair evidence.

The GTDB Toolkit (GTDB-Tk) provides objective taxonomic assignments for bacterial and archaeal genomes based on the Genome Taxonomy Database (GTDB)

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins

HUMAnN is a pipeline for efficiently and accurately profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data (typically millions of short DNA/RNA reads).

IIBacFinder (class II bacteriocin finder) is designed to detect class II bacteriocins (small, unmodified antimicrobial peptides).

Infernal (INFERence of RNA ALignment) is for searching DNA sequence databases for RNA structure and sequence similarities. It is an implementation of a special case of profile stochastic context-free grammars called covariance models (CMs). A CM is like a sequence profile, but it scores a combination of sequence consensus and RNA secondary structure consensus, so in many cases, it is more capable of identifying RNA homologs that conserve their secondary structure more than their primary sequence.

integrated Phage Host Prediction. It is an automated command-line pipeline for predicting host genus of novel bacteriophages and archaeoviruses based on their genome sequences.

Efficient software for phylogenomic inference

Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA.

Je is a suite to handle barcoded fastq files with (or without) Unique Molecule Identifiers (UMIs) and filter read duplicates using these UMIs

KAT provides a suite of tools that, through the use of k-mer counts, help the user address or identify issues such as determining sequencing completeness for assembly, assessing sequencing bias, identifying contaminants, validating genomic assemblies and filtering content.

Create BIOM-format tables from Kraken output

taxonomic sequence classification system

KrakenTools is a suite of scripts to be used for post-analysis of Kraken/KrakenUniq/Kraken2/Bracken results

Krona allows hierarchical data to be explored with zoomable pie charts. Krona charts can be created using an Excel template or KronaTools

Fast and sensitive variant-caller for inferring SNVs and indels

LTR_retriever is a highly accurate and sensitive program for identification of LTR retrotransposons; The LTR Assembly Index (LAI) is also included in this package.

Model-based Analysis for ChIP-Seq

Model-based Analysis for ChIP-Seq

MaxBin is a software that is capable of clustering metagenomic contigs into different bins, each consists of contigs from one species.

The Molecular Evolutionary Genetics Analysis (MEGA) software is developed with the goal of providing a biologist centric, integrated suite of tools for statistical analyses of DNA and protein sequence data from an evolutionary standpoint.

Software for analyzing metagenomes

Evaluate genome assemblies with k-mers and more

Meryl is a tool for creating and working with DNA sequence k-mers. K-mers are typically created by counting how many times each k-mer sequence occurs in some collection of sequences. Meryl refers to this as the value of the k-mer.

MetaBAT is an automated metagenome binning software which integrates empirical probabilistic distances of genome abundance and tetranucleotide frequency.

read quality control, assembly, visualization, taxonomic profiling, extracting draft genomes (binning), and functional annotation

a software suite to search and cluster huge sequence sets

Software suite to search and cluster huge protein and nucleotide sequence sets

MobiDB-lite, long disorder consensus predictor

Aggregate results from bioinformatics analyses across many samples into a single report.

Generate graphs from a distance matrix

Plotting tool for long read sequencing data and alignments

OMArk is a software for proteome (protein-coding gene repertoire) quality assessment.

ONT-AmpSeq is a complete Snakemake workflow, designed to generate OTU-tables from demultiplexed amplicon data

A program for aligning short reads to reference phylogenies and alignments

PEAR is an ultrafast, memory-efficient and highly accurate pair-end read merger. It is fully parallelized and can run with as low as just a few kilobytes of memory.

A suite of tools to build and search generalized profiles.

PHAST is a fast phage search tool.

PhyloPhlAn is an integrated pipeline for large-scale phylogenetic profiling of genomes and metagenomes.

A set of tools in Java for working with NGS data in the BAM format

POD5 is a file format for storing nanopore dna data in an easily accessible way.

Prodigal provides fast, accurate protein-coding gene predictions in GFF3, Genbank, or Sequin table format. It does not need to be provided with any training data, and instead automatically learns the properties of the genome from the sequence itself, including RBS motif usage, start codon usage, and coding statistics. Handles gaps and partial genes.

PSORTb is a precise bacterial localization prediction tool.

Haplotypic duplication identification tool

A simple pipeline for reassigning primary contigs that should be labelled as haplotigs.

Python package and standalone program for calculation of whole-genome similarity measures

Redesigned and improved ChIP-seq broad peak calling tool SICER

pipeline for performing microbiome analysis from raw DNA sequencing data

In development.

Quasitools is a collection of tools for analysing viral quasispecies data.

RASflow is a modular, flexible and user-friendly RNA-Seq analysis workflow.

RAxML-NG is a phylogenetic tree inference tool which uses maximum-likelihood (ML) optimality criterion

Randomized Axelerated Maximum Likelihood

RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences

RepeatModeler is a de novo transposable element (TE) family identification and modeling package. At the heart of RepeatModeler are three de-novo repeat finding programs ( RECON, RepeatScout and LtrHarvest/Ltr_retriever ) which employ complementary computational methods for identifying repeat element boundaries and family relationships from sequence data.

The rMATS-turbo software is a general-purpose computational tool for analyzing alternative splicing using short-read RNA-seq data

RMBlast is a RepeatMasker compatible version of the standard NCBI blastn program

high performance highly parallel robust and fast tool (and library), written in the D programming language, for working with SAM and BAM files

Samblaster is a fast and flexible program for marking duplicates in read-id grouped1 paired-end SAM files. It can also optionally output discordant read pairs and/or split read mappings to separate SAM files, and/or unmapped/clipped reads to a separate FASTQ file.

Redesigned and improved ChIP-seq broad peak calling tool SICER

The SignalP 5.0 server predicts the presence of signal peptides and the location of their cleavage sites in proteins from Archaea, Gram-positive Bacteria, Gram-negative Bacteria and Eukarya. SignalP 5.0 is based on a deep convolutional and recurrent neural network architecture including a conditional random field.

Rapid haploid variant calling and core genome alignment

SNPTEST is a program for the analysis of single SNP association in genome-wide studies. The tests implemented include.

SortMeRNA is a local sequence alignment tool for filtering, mapping and clustering.

Space Ranger is a set of analysis pipelines that process 10x Genomics Visium data with brightfield or fluorescence microscope images

Squeezemeta is a fully automated metagenomics pipeline, from reads to bins

STAR is an ultrafast universal RNA-seq aligner

sylph is a program that performs ultrafast (1) ANI querying or (2) metagenomic profiling for metagenomic shotgun samples

Syri compares alignments between two chromosome-level assemblies and identifies synteny and structural rearrangements

A package for including transposable elements in differential enrichment analysis of sequencing datasets.

a program to analyze DNA sequences

A tool for automated aligment trimming

a tool for finding transfer RNAs

VarRNA is a comprehensive pipeline designed to process RNA-Seq reads from tumor samples, starting with either FASTQ or BAM files. It identifies single nucleotide variants (SNVs) and indels, and classifies these variants as germline, somatic, or artifact.

Variation graphs provide a succinct encoding of the sequences of many genomes. A variation graph (in particular as implemented in vg).

VILOCA is an open source project for the analysis of next generation sequencing data. It is designed to analyse genetically heterogeneous samples. Its tools are written in different programming languages and provide error correction, haplotype reconstruction and estimation of the frequency of the different genetic variants present in a mixed sample.

Virathon is designed to automate the analysis of genomic sequences derived from viruses of Archaea and Bacteria, specially uncultured ones originated from metagenomic samples

ViReMa (Viral Recombination Mapper) detects and reports recombination or fusion events in virus genomes using deep sequencing datasets.

A multi-classifier, expert-guided approach to detect diverse DNA and RNA virus genomes

a low-frequency virus variant detection pipeline for Illumina sequencing using adaptive base-calling accuracy filtering

Predict prokaryotic host for phage metagenomic sequences

A bisulfite read mapper and methylation caller

Read mapping utility

A Genomic Mapping and Alignment Program for mRNA and EST sequences.

HISAT is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA)

Multiple alignment program for amino acid or nucleotide sequences

Stereo-seq Analysis Workflow (SAW) software suite is a set of pipelines bundled to map sequenced reads to their spatial location on the tissue section, quantify spatial feature expression, and visually present spatial expression distribution.

Legacy blast, it is better to use blast_plus

find matches between input and databases

fast sequence search command line tool

Bwa-mem2 is the next version of the bwa-mem algorithm in bwa.

Fast, scalable generation of high-quality protein multiple sequence alignments

Accelerated BLAST compatible local sequence aligner

DRAGMAP is a new mapper for Illumina reads. It is like a CPU-only implementation of the DRAGEN mapping algorithm.

Sequence compare tool

HMMER is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments.

LASTZ (Large-Scale Genome Alignment Tool) is a fast and powerful alignment tool for the pairwise alignment of genomic DNA sequence

Unlike most mapping tools, Magic-BLAST does not build an index of a genome and instead it builds an index of a batch of reads and scans a BLAST database for potential matches. BLAST database can be created from a FASTA file in seconds or minutes instead of hours for most indices. It also allows for mapping to or searching arbitrarily large collections of sequences.

Platypus is a tool designed for efficient and accurate variant-detection in high-throughput sequencing data

Performs a full rigid-body search of docking orientations between two proteins. .

BBMap short read aligner, and other bioinformatic tools.

CD-HIT sequence clustering

Cell Ranger is a set of analysis pipelines that process Chromium single cell data to align reads, generate feature-barcode matrices, perform clustering and other secondary analysis, and more

Rust implementation of NanoFilt+NanoLyse, both originally written in Python. This tool, intended for long read sequencing such as PacBio or ONT, filters and trims a fastq file.

Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your NGS reads

deepTools is a suite of python tools particularly developed for the efficient analysis of high-throughput sequencing data, such as ChIP-seq, RNA-seq or MNase-seq.

A tool designed to provide fast all-in-one preprocessing for FastQ files

fastq-mcf sequence quality filter, clipping and processor.

A quality control tool for high throughput sequence data.

Full length sequences

Chromatogram preprocessing

RiboDetector is a software developed to accurately yet rapidly detect and remove rRNA sequences from metagenomeic, metatranscriptomic, and ncRNA sequencing data.

ultrafast toolkit for FASTAQ file manipulation

Sequence preprocessing and trimming

NGS sequencing preprocessing

Trim Galore is a wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS data.

A flexible read trimming tool for Illumina NGS data

RNA-seq assembler and analyzer

Estimates gene and isoform expression levels from RNA-Seq data with a statistical model that takes into account reads that map to multiple positions

Transcriptome assembly software

AI system developed by DeepMind that predicts a protein’s 3D structure from its amino acid sequence

A COMprehensive Platform for Small RNA-seq data AnalySis

A Python library to facilitate programmatic analysis of data from high-throughput sequencing (HTS) experiments. A popular component of HTSeq is htseq-count, a script to quantify gene expression in bulk and single-cell RNA-Seq and similar experiments

Near-optimal RNA-Seq quantification

process a coordinate-sorted and indexed BAM or CRAM file containing some form of BS-seq alignments and extract per-base methylation metrics from them

Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment

Toolkit for processing next-gen sequencing data. It includes Subread aligner, Subjunc exon-exon junction detector and featureCounts.

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

prediction and comparison of RNA secondary structures.