Programs for NGS work
| Application purpose | Name | Short description | Links |
|---|---|---|---|
| ChIP-Seq | MACS2 | Model-based Analysis of ChIP-Seq data for identifying transcript factor binding sites | homepage |
| Hi-C | FitHiChIP | Statistically Significant loops from HiChIP data | homepage, publication |
| HiC-Pro | HiC-Pro: An optimized and flexible pipeline for Hi-C data processing | documentation, publication | |
| hichipper | hichipper is a command-line toolkit that performs restriction fragment bias-aware preprocessing of HiChIP data. | homepage, documentation | |
| RADseq | ipyrad | interactive assembly and analysis of RADseq data sets | documentation |
| pyRAD | assembly of de novo RADseq loci for phylogenetic analyses | publication | |
| SNP | Snippy | Rapid haploid variant calling and core genome alignment | homepage |
| SNPiR | a suite of tools for reliable identification of genomic variants using RNA-seq data | publication | |
| Subread | High-performance read alignment, quantification and mutation discovery. The package contains the programs Subread, Subjunc, featureCounts, Sublong and exactSNP. | homepage | |
| analysis | Cufflinks | assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples | homepage |
| deepTools | command-line tools to process and analyze deep sequencing data | homepage | |
| DESeq | differential gene expression of RNA-seq data at the gene level | publication, homepage | |
| exomePeak | exome-based analysis for RNA epigenome sequencing data | publication, homepage | |
| Geneious | a powerful and comprehensive suite of molecular biology and NGS analysis tools with very good visualization | homepage | |
| Hail | Hail is an open-source, scalable framework for exploring and analyzing genomic data. | homepage | |
| HOMER | suite of tools for Motif Discovery and next generation sequencing analysis | homepage | |
| ipyrad | interactive assembly and analysis of RADseq data sets | documentation | |
| kallisto | program for quantifying abundances of transcripts from RNA-Seq data | homepage, publication | |
| Katuali | Katuali is a flexible consensus pipeline implemented in Snakemake to basecall, assemble, and polish Oxford Nanopore Technologies' sequencing data. | homepage, documentation | |
| Loupe Cell Browser | A desktop application for Windows and MacOS that allows you to quickly and easily visualize and analyze 10x Chromium Single Cell 5' and 3' gene expression data. | homepage | |
| MACS2 | Model-based Analysis of ChIP-Seq data for identifying transcript factor binding sites | homepage | |
| MarkerMiner | fully automated workflow and application for discovery of SCN loci in angiosperms | homepage, publication | |
| miRDeep2 | A tool for discovering known and novel miRNAs from small RNA sequencing data. | documentation, publication, tutorial | |
| miRExpress | tool to analyze high-throughput sequencing data for profiling microRNA expression | homepage, publication | |
| mirPRo | a novel standalone program for differential expression and variation analysis of miRNAs | homepage, publication | |
| Pomoxis | Pomoxis comprises a set of basic bioinformatic tools tailored to nanopore sequencing. | documentation | |
| RSEM | accurate transcript quantification from RNA-Seq data with or without a reference genome | publication | |
| Salmon | A tool for quantifying the expression of transcripts using RNA-seq data. | homepage | |
| SNPiR | a suite of tools for reliable identification of genomic variants using RNA-seq data | publication | |
| Staden Package | tools for DNA sequence assembly, editing and sequence analysis | homepage | |
| annotation | Hail | Hail is an open-source, scalable framework for exploring and analyzing genomic data. | homepage |
| assembly | ABySS | parallel assembler for short read sequence data | publication, tutorial |
| ALLPATHS-LG | short read genome assembler | homepage, tutorial | |
| AMOS | modular open source whole genome assembler | publication, tutorial | |
| BinPacker | packing-based de novo transcriptome assembly from RNA-seq data | publication | |
| Canu | Canu is a fork of the Celera Assembler designed for high-noise single-molecule sequencing (such as the PacBio RSII or Oxford Nanopore MinION). | documentation | |
| Celera Assembler | de novo whole-genome shotgun (WGS) DNA sequence assembler | homepage | |
| Cufflinks | assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples | homepage | |
| DETONATE | de novo transcriptome RNA-seq assembly | homepage | |
| Flye | Flye is a de novo assembler for single molecule sequencing reads. | homepage | |
| Geneious | a powerful and comprehensive suite of molecular biology and NGS analysis tools with very good visualization | homepage | |
| IDBA | de novo assembler for short reads sequencing data with highly uneven sequencing depths | homepage | |
| ipyrad | interactive assembly and analysis of RADseq data sets | documentation | |
| KisSplice | local transcriptome assembler for SNPs, indels and AS events | homepage | |
| MARVEL | MARVEL consists of a set of tools that facilitate the overlapping, patching, correction and assembly of noisy (not so noisy ones as well) long reads. | homepage | |
| Miniasm | Ultrafast de novo assembly for long noisy reads (though having no consensus step) | homepage | |
| MIRA | a multi-pass DNA sequence data assembler/mapper for whole genome and EST/RNA-seq projects | homepage | |
| Nanopolish | Software package for signal-level analysis of Oxford Nanopore sequencing data | manual | |
| Oases | de novo transciptome assembler for very short reads | homepage, publication | |
| Pilon | Pilon is an automated genome assembly improvement and variant detection tool. | homepage | |
| Platanus | PLATform for Assembling NUcleotide Sequences is a novel de novo sequence assembler that can reconstruct genomic sequences of highly heterozygous diploids from massively parallel shotgun sequencing data | homepage, publication | |
| pyRAD | assembly of de novo RADseq loci for phylogenetic analyses | publication | |
| Racon | ultrafast consensus module for raw de novo genome assembly of long uncorrected reads | publication, tutorial | |
| Scallop | Scallop is a reference-based transcriptome assembler for RNA-seq. | homepage, publication | |
| SMARTdenovo | Ultra-fast de novo assembler using long noisy reads. | homepage | |
| SOAPdenovo | de novo short reads assembler | homepage | |
| SOAPdenovo-Trans | A de novo transcriptome assembler designed specifically for RNA-Seq. | homepage, publication | |
| SPAdes | An assembly toolkit containing various assembly pipelines. | homepage, manual | |
| Staden Package | tools for DNA sequence assembly, editing and sequence analysis | homepage | |
| Trans-ABySS | de novo assemly of RNA-Seq data | homepage, publication | |
| Transrate | software for de-novo transcriptome assembly quality analysis | homepage | |
| TRINITY | de novo reconstruction of transcriptomes from RNA-Seq data | homepage, publication | |
| Velvet | sequence assembler for very short reads | homepage | |
| wtdbg2 | A de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies. | homepage | |
| counting | Subread | High-performance read alignment, quantification and mutation discovery. The package contains the programs Subread, Subjunc, featureCounts, Sublong and exactSNP. | homepage |
| filter/trimming | Cutadapt | searches for the adapter in all reads and removes it when found | publication, tutorial |
| Filtlong | Filtlong is a tool for filtering long reads by quality. | homepage | |
| Nanofilt | Filtering and trimming of long read sequencing data | homepage, publication | |
| Porechop | adapter trimmer for Oxford Nanopore reads | homepage | |
| SortMeRNA | a program tool for filtering, mapping and OTU-picking NGS reads in metatranscriptomic and metagenomic data | homepage | |
| Trim Galore! | wrapper tool around Cutadapt and FastGC to consistently apply quality and adapter trimming to FastQ files | homepage | |
| Trimmomatic | flexible trimmer for Illumina NGS data | homepage | |
| genome browser | Pauvre | QC and genome browser plotting Oxford Nanopore and PacBio long reads | homepage |
| genomics | JMP Genomics | advanced genomic data analysis software with very good visualization (part of the SAS-JMP-bundle) | homepage |
| molecular biology | Geneious | a powerful and comprehensive suite of molecular biology and NGS analysis tools with very good visualization | homepage |
| nanopore sequencing | Canu | Canu is a fork of the Celera Assembler designed for high-noise single-molecule sequencing (such as the PacBio RSII or Oxford Nanopore MinION). | documentation |
| Flappie | Flip-flop basecaller for Oxford Nanopore reads. | homepage | |
| Flye | Flye is a de novo assembler for single molecule sequencing reads. | homepage | |
| Guppy | Accelerated basecaller for Oxford Nanopore Sequencing | homepage | |
| Katuali | Katuali is a flexible consensus pipeline implemented in Snakemake to basecall, assemble, and polish Oxford Nanopore Technologies' sequencing data. | homepage, documentation | |
| MARVEL | MARVEL consists of a set of tools that facilitate the overlapping, patching, correction and assembly of noisy (not so noisy ones as well) long reads. | homepage | |
| Medaka | Medaka is a tool to create a consensus sequence from nanopore sequencing data. | homepage, documentation | |
| Miniasm | Ultrafast de novo assembly for long noisy reads (though having no consensus step) | homepage | |
| Minimap2 | A versatile pairwise aligner for genomic and spliced nucleotide sequences | homepage, publication, manual | |
| Nanofilt | Filtering and trimming of long read sequencing data | homepage, publication | |
| Nanopolish | Software package for signal-level analysis of Oxford Nanopore sequencing data | manual | |
| NanoStat | Create statistic summary of an Oxford Nanopore read dataset | homepage, publication | |
| Pauvre | QC and genome browser plotting Oxford Nanopore and PacBio long reads | homepage | |
| Pomoxis | Pomoxis comprises a set of basic bioinformatic tools tailored to nanopore sequencing. | documentation | |
| Porechop | adapter trimmer for Oxford Nanopore reads | homepage | |
| poretools | toolkit for working with nanopore sequencing data from Oxford Nanopore | homepage | |
| Scrappie | Basecaller for Oxford Nanopore Sequencing | homepage | |
| Shasta | De novo assembly from Oxford Nanopore reads. | documentation | |
| SMARTdenovo | Ultra-fast de novo assembler using long noisy reads. | homepage | |
| wtdbg2 | A de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies. | homepage | |
| phylogenetics | fastStructure | A variational framework for inferring population structure from SNP genotype data. | homepage, publication |
| MarkerMiner | fully automated workflow and application for discovery of SCN loci in angiosperms | homepage, publication | |
| POPBAM | tools for evolutionary analysis of short read sequence alignments | publication | |
| pyRAD | assembly of de novo RADseq loci for phylogenetic analyses | publication | |
| quality control | BUSCO | quantitative measures for the assessment of genome assembly, gene set, and transcriptome completeness | homepage, publication |
| FastQC | quality control tool for high throughput sequence data | homepage | |
| Hail | Hail is an open-source, scalable framework for exploring and analyzing genomic data. | homepage | |
| hichipper | hichipper is a command-line toolkit that performs restriction fragment bias-aware preprocessing of HiChIP data. | homepage, documentation | |
| LoRDEC | LoRDEC is a program to correct sequencing errors in long reads from 3rd generation sequencing with high error rate, and is especially intended for PacBio reads. | homepage | |
| QUAST | QUAST stands for QUality ASsessment Tool. The tool evaluates genome assemblies by computing various metrics. | homepage, manual | |
| RSeQC | a package that provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data | homepage | |
| Transrate | software for de-novo transcriptome assembly quality analysis | homepage | |
| Trim Galore! | wrapper tool around Cutadapt and FastGC to consistently apply quality and adapter trimming to FastQ files | homepage | |
| scaffolding | BESST | scaffolding of large fragmented assemblies | publication, tutorial |
| GapFiller | stand-alone program for closing gaps within pre-assembled scaffolds | publication | |
| SSPACE-LongRead | a program for scaffolding longreads (e.g. PacBio RS reads) | homepage, publication | |
| SSPACE-Standard | a program for scaffolding pre-assembled contigs using NGS paired-read data | homepage, publication | |
| sequence alignment | BamTools | command-line toolkit for for handling genome alignment files | tutorial |
| BBMap | a splice-aware global aligner for DNA and RNA sequencing reads | homepage, tutorial | |
| Bowtie 1 | ultrafast, memory-efficient short read aligner | homepage | |
| Bowtie 2 | ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences | homepage | |
| Burrows-Wheeler Aligner | software package for mapping low-divergent sequences against a large reference genome | homepage | |
| Cell Ranger | A set of analysis pipelines that process Chromium single cell 3' RNA-seq output to align reads, generate gene-cell matrices and perform clustering and gene expression analysis. For viewer software, see Loupe Cell Browser. | homepage | |
| Geneious | a powerful and comprehensive suite of molecular biology and NGS analysis tools with very good visualization | homepage | |
| HISAT2 | A fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome). | homepage | |
| Minimap2 | A versatile pairwise aligner for genomic and spliced nucleotide sequences | homepage, publication, manual | |
| Samtools | various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format | homepage | |
| SOAPaligner | alignment tool | homepage | |
| STAR | Spliced Transcript Alignment to a Reference: fast RNA-seq read mapper | homepage | |
| Subread | High-performance read alignment, quantification and mutation discovery. The package contains the programs Subread, Subjunc, featureCounts, Sublong and exactSNP. | homepage | |
| TopHat | fast splice junction mapper for RNA-Seq reads that aligns RNA-Seq reads to mammalian-sized genomes using Bowtie | homepage | |
| wtdbg2 | A de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies. | homepage | |
| single cell analysis | Cell Ranger | A set of analysis pipelines that process Chromium single cell 3' RNA-seq output to align reads, generate gene-cell matrices and perform clustering and gene expression analysis. For viewer software, see Loupe Cell Browser. | homepage |
| Cicero | Cicero is an R package that provides tools for analyzing single-cell chromatin accessibility experiments. | homepage | |
| special purpose | BUSCO | quantitative measures for the assessment of genome assembly, gene set, and transcriptome completeness | homepage, publication |
| DEXSeq | package for finding differential exon usage using RNA-seq exon counts | publication, homepage | |
| eXpress | streaming fragment assignment and quantification for high-throughput sequencing | homepage | |
| Geneious | a powerful and comprehensive suite of molecular biology and NGS analysis tools with very good visualization | homepage | |
| miRDeep2 | A tool for discovering known and novel miRNAs from small RNA sequencing data. | documentation, publication, tutorial | |
| miRExpress | tool to analyze high-throughput sequencing data for profiling microRNA expression | homepage, publication | |
| mirPRo | a novel standalone program for differential expression and variation analysis of miRNAs | homepage, publication | |
| SortMeRNA | a program tool for filtering, mapping and OTU-picking NGS reads in metatranscriptomic and metagenomic data | homepage | |
| Stacks | software pipeline for building loci from short-read sequences | homepage, publication | |
| toolkit | FASTX | collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing | homepage |
| Hail | Hail is an open-source, scalable framework for exploring and analyzing genomic data. | homepage | |
| HOMER | suite of tools for Motif Discovery and next generation sequencing analysis | homepage | |
| NCBI-TOOLS | more than 700 tools, e.g. for downloading custom data sets | homepage | |
| poretools | toolkit for working with nanopore sequencing data from Oxford Nanopore | homepage | |
| utilities | BCFtools | utilities for variant calling and manipulating VCFs and BCFs | homepage, tutorial |
| bcl2fastq | demultiplexes data and converts BCL files generated by Illumina sequencing systems to standard FASTQ file formats | homepage | |
| HTSeq | Python package that provides infrastructure to process data from high-throughput sequencing assays | publication, homepage | |
| Samtools | various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format | homepage | |
| SRA-Toolkit | toolkit to convert .sra files into other formats | publication | |
| variants | BCFtools | utilities for variant calling and manipulating VCFs and BCFs | homepage, tutorial |
| GATK | toolkit for variant discovery in high-throughput sequencing data | homepage | |
| Pilon | Pilon is an automated genome assembly improvement and variant detection tool. | homepage | |
| Snippy | Rapid haploid variant calling and core genome alignment | homepage | |
| SNPiR | a suite of tools for reliable identification of genomic variants using RNA-seq data | publication | |
| SVDetect | SVDetect is a application for the isolation and the type prediction of intra- and inter-chromosomal rearrangements from paired-end/mate-pair sequencing data. | homepage, manual | |
| visualization | Geneious | a powerful and comprehensive suite of molecular biology and NGS analysis tools with very good visualization | homepage |
| Hail | Hail is an open-source, scalable framework for exploring and analyzing genomic data. | homepage | |
| HiC-Pro | HiC-Pro: An optimized and flexible pipeline for Hi-C data processing | documentation, publication | |
| JMP Genomics | advanced genomic data analysis software with very good visualization (part of the SAS-JMP-bundle) | homepage | |
| Loupe Cell Browser | A desktop application for Windows and MacOS that allows you to quickly and easily visualize and analyze 10x Chromium Single Cell 5' and 3' gene expression data. | homepage | |
| ngs.plot | a standalone program to visualize enrichment patterns of DNA-interacting proteins at functionally important regions based on NGS data. | publication |
last modified: 14.05.2020 - 11:04