ENCODE Software
All software used or developed by the ENCODE Consortium
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- Distal Regulation E-G correlation — sourceCompute correlation metrics between DNase-seq signal at cCREs with DNase-seq signal at gene promoters or RNA expression levels of genes.
- Distal regulation ENCODE-rE2G — sourceTrain ENCODE-rE2G models on CRISPR enhancer screen data and apply to generate genome-wide predictions of enhancer-gene regulatory connections.
- mex_gene_archive — sourcemex_gene_archive is a minimal file format designed to meet the needs of archiving sparse gene matrices in a format compatible with the ENCODE 4 Data Coordination Center.Software type: other
- OpenMiChrom — sourceUsed to create an ensemble of 3D structures with chromatin dynamics simulation software with input data from the Sequence Annotations (bed file) from PyMEGABASE.
- PyMEGABASE — sourcePyMEGABASE is used to generate sequence annotations at the compartment and subcompartment level for physical modeling annotations.
- pyrangesGenomicRanges for Python.
- pandasPandas is a fast, powerful, flexible and easy to use open source data analysis and manipulation tool, built on top of the Python programming language.
- SwanSwan is a Python library designed for the analysis and visualization of transcriptomes.Software type: other
- ABC-Enhancer-Gene-Prediction — sourceCell type specific enhancer-gene predictions using ABC model (Fulco, Nasser et al, Nature Genetics 2019)
- AnalyzeSpearATACSoftware used to analyze Greenleaf lab's SpearATAC (perturbation followed by snATAC-seq) data.
- CerberusCerberus software for long-read RNA-seq analysisSoftware type: other
- CRISPRi-FlowFISHSoftware for the analysis of CRISPRi-FlowFISH data from Engreitz lab.
- GraphReg — sourceGraphReg (Chromatin interaction aware gene regulatory modeling with graph attention networks) is a graph neural network based gene regulation model which integrates DNA sequence, 1D epigenomic data (such as chromatin accessibility and histone modifications), and 3D chromatin conformation data (such as Hi-C, HiChIP, Micro-C, HiCAR) to predict gene expression in an informative way.
- HiCDCPlus — sourceThe package HiCDCPlus provides methods to determine significant and differential chromatin interactions by use of a negative binomial generalized linear model, as well as implementations for TopDom to call topologically associating domains (TADs), and Juicer eigenvector to find the A/B compartments. This vignette explains the use of the package and demonstrates typical workflows on HiC and HiChIP data.
- ZeroneZerone discretizes several ChIP-seq replicates simultaneously and resolves conflicts between them. Publication available at: doi: 10.1093/bioinformatics/btw336
- GEM-ToolsGEM-Tools is a C API and a Python module to support and simplify usage of the GEM Mapper.
- Fastx Toolkit — sourceThe FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing.
- TRACETranscription Factor Footprinting Using DNase I Hypersensitivity Data and DNA Sequence
- 3d-dna — sourceWe begin with a series of iterative steps whose goal is to eliminate misjoins in the input scaffolds. Each step begins with a scaffold pool (initially, this pool is the set of input scaffolds themselves). The scaffolding algorithm is used to order and orient these scaffolds. Next, the misjoin correction algorithm is applied to detect errors in the scaffold pool, thus creating an edited scaffold pool. Finally, the edited scaffold pool is used as an input for the next iteration of the misjoin correction algorithm. The ultimate effect of these iterations is to reliably detect misjoins in the input scaffolds without removing correctly assembled sequence. After this process is complete, the scaffolding algorithm is applied to the revised input scaffolds, and the output – a single “megascaffold” which concatenates all the chromosomes – is retained for post-processing.
- bioraddbg ATAC-seq MACS2 — sourceThis Docker container provides an easy to use Docker interface to MACS2 for peak calling with settings tailored for Bio-Rad Single Cell ATAC-seq chemistry.
- bioraddbg ATAC-seq filter beads — sourceThis Docker container provides an easy to use Docker interface to a bead filtration tool with settings tailored for Bio-Rad Single Cell ATAC-seq chemistry. This container takes in .BAM files and performs "knee calling" to compute a bead barcode whitelist and jaccard index threshold for bead-to-droplet merging.
- bioraddbg ATAC-seq BWA — sourceThis Docker container provides an easy to use Docker interface to the BWA alignment tool with settings tailored for Bio-Rad ATAC-Seq chemistry.
- bioraddbg ATAC-seq deconvolute — sourceThis Docker container provides an easy to use Docker interface to BAP tool with settings tailored for Bio-Rad ATAC-seq chemistry.
- guppy_basecaller — sourceOnt-Guppy is a basecalling software available to Oxford Nanopore customers. For more information, please see https://nanoporetech.com/
- polyAsite_workflow — sourcePipeline to infer poly(A) site clusters through processing of 3' end sequencing libraries prepared according to various protocols.
- gencode_utr_fix — sourceThis package fixes UTR features in the third columns of Gencode GTF by converting UTR annotation into five_prime_utr and three_prime_utr similar to Ensembl.
- split-pipe — sourceThe Parse Biosciences computational pipeline is an out-of-the-box software tool that you can run locally to convert fastq files straight to processed data (including gene-cell count matrices). Customers purchasing the Whole Transcriptome Kit will receive access to the Parse computational pipeline.
- PRINSEQ Lite — sourcePRINSEQ will preprocess genomic or metagenomic sequence data in FASTA or FASTQ format
- sQTLseekeR — sourcesQTLseekeR is a package to detect splicing QTLs (sQTLs), which are variants associated with change in the splicing pattern of a gene. In sQTLSeeker, splicing patterns are modeled by the relative expression of the transcripts of a gene. The most recent version of sQTLseekeR can be employed to detect genetic variant associated to any multivariate phenotypeSoftware type: variant annotation
- ggsashimi — sourcea command-line tool for the visualization of splicing events across multiple samples. Given a specified genomic region, ggsashimi creates sashimi plots for individual RNA-seq experiments as well as aggregated plots for groups of experiments. It uses popular bioinformatics file formats, it is annotation-independent, and allows the visualization of splicing events even for large genomic regions by scaling down the genomic segments between splice sites. It is implemented in python, and internally generates R code for plotting.Software type: visualization
- Library sequencing match — sourceHouse script that was matching the guides (from an input list) to the fastq files as returned by deep sequencingSoftware type: quantification
- eFORGE — sourceeFORGE identifies tissue or cell type-specific signal by analysing a minimum set of 5 differentially methylated positions (DMPs) for overlap with DNase I hypersensitive sites (DHSs) compared to matched background DMPs and provides both graphical and tabulated outputs.Software type: integrated analysis
- GenomeStudio — sourceSoftware developed by Illumina for analysis of microarray data.Software type: other
- CRISPR screen peak calling — sourceTakes CASA output and makes ENCODE sandard element quantification fileSoftware type: file format conversion
- CRISPR screen track builder — sourceTakes guide quantification and builds a browser track perturbation signal fileSoftware type: quantification
- ptools_bin — sourceA data-sanitization software allowing raw functional genomics reads to be shared while minimizing privacy leakage, enabling principled privacy-utility trade-offs.Software type: other
- SCREEN — sourceSCREEN is a web-based visualizer for the ENCODE Registry of cCREs. Users can search for cCREs by genomic region or by associated features such as genes and SNPs, and can also visualize associated underlying annotations from the ground and integrative levels of the ENCODE Encyclopedia such as gene expression, TF ChIP-seq peaks, chromatin states, and cCRE-target gene links. Additionally, users can access ENCODE data on the functional characterization of cCREs.
- apricot — sourceapricot implements submodular optimization for the purpose of summarizing massive data sets into minimally redundant subsets that are still representative of the original data. These subsets are useful for both visualizing the modalities in the data and for training accurate machine learning models with just a fraction of the examples and compute.
- CRADLE — sourceCRADLE (Correcting Read counts and Analysis of DifferentiaLly Expressed regions) is a package that was developed to analyze STARR-seq data. CRADLE removes technical biases from sonication, PCR, mappability and G-quadruplex sturcture, and generates bigwig files with corrected read counts. CRADLE then uses those corrected read counts and detects both activated and repressed enhancers. CRADLE will help find enhancers with better accuracy and credibility.
- Croo — sourceCroo is a Python package for organizing outputs from Cromwell. Croo parses metadata.json which is an output from Cromwell and makes an organized directory with a copy (or a soft link) of each output file as described in an output definition JSON file specified by --out-def-json.Software type: framework
- Caper — sourceCaper (Cromwell Assisted Pipeline ExecutoR) is a wrapper Python package for Cromwell. Caper is based on Unix and cloud platform CLIs (curl, gsutil and aws) and provides easier way of running Cromwell server/run modes by automatically composing necessary input files for Cromwell. Also, Caper supports easy automatic file transfer between local/cloud storages (local path, s3://, gs:// and http(s)://). You can use these URIs in input JSON file or for a WDL file itself.Software type: framework
- encode_utils — sourceTools that are useful to any ENCODE Consortium submitting group, as well as the general community working with ENCODE data. Library and scripts are coded in Python.
- Check Files — sourceFiles are checked to see if the MD5 sum (both for gzipped and ungzipped) is identical to the submitted metadata, as well as run through the validateFiles program from Jim Kent's source utilities.
- liftOverThis UCSC tool converts genome coordinates and genome annotation files between assemblies.
- eCLIP core pipeline — sourceCustom software developed by Yeo lab for use in the eCLIP pipeline.Software type: other
- fastq-tools — sourceA collection of small and efficient programs for performing some common and uncommon tasks with FASTQ files.Software type: other
- mpraflow-tsv-to-bedThis is a one-line custom Perl script used to generate a bed format file from tsv.
- FASTQ read-name correctionA script resolving FASTQ read-name inconsistencies
- scPOST — sourceSimulation of single-cell datasets for power analyses that estimate power to detect cell state frequency shifts between conditions (e.g. an expansion of a cell state in disease vs. healthy), as described in our manuscript “Maximizing statistical power to detect clinically associated cell states with scPOST”.Software type: other
- cdr3-QTL — sourceWe tested associations between HLA genotypes and TCR-CDR3 amino acid compositions. We treated the amino acid composition of CDR3 as a quantitative trait, and tested its association with HLA genotype; we call this CDR3 quantitative trait loci analysis (cdr3-QTL), as described in our manuscript “HLA autoimmune risk alleles restrict the hypervariable region of T cell receptors”.Software type: other
- Imperio — sourceThis software includes (i) DeepBoost, a gradient boosting method for constructing boosted deep learning annotations by integrating deep learning allelic-effect annotations with fine-mapped SNPs; (ii) tools to combine these deep learning annotations with SNP-to-gene (S2G) linking strategies and relevant gene sets, and (iii) Imperio, a method for integrating deep learning annotations with S2G strategies to predict gene expression in whole blood and construct allelic-effect annotations based on changes in predicted expression. Applications of these 3 approaches to blood-related traits are described in our manuscript “Integrative approaches to improve the informativeness of deep learning models for human complex diseases”.Software type: other
- GSSG — sourceGSSG consists of tools to generate enhancer-driven and master-regulator gene scores in blood, and combine these gene scores with distal and proximal SNP-to-gene (S2G) linking strategies to construct SNP annotations for blood-related traits, as described in our manuscript “Unique contribution of enhancer-driven and master-regulator genes to autoimmune disease revealed using functionally informed SNIP-to-gene linking strategies”.Software type: other
- AnnotBoost — sourceAnnotBoost is a gradient boosting-based framework to impute and denoise Mendelian disease-derived pathogenicity scores to improve their informativeness for common disease, as described in our manuscript “Improving the informativeness of Mendelian disease-derived pathogenicity scores for common disease”.Software type: variant annotation
- ChromImpute — sourceChromImpute is software for large-scale systematic epigenome imputation. ChromImpute takes an existing compendium of epigenomic data and uses it to predict signal tracks for mark-sample combinations not experimentally mapped or to generate a potentially more robust version of data sets that have been mapped experimentally. ChromImpute bases its predictions on features from signal tracks of other marks that have been mapped in the target sample and the target mark in other samples with these features combined using an ensemble of regression trees.
- Bru-seq ToolsThe Ljungman lab scripts used to process Bru-seq, BruUV-seq, and BruChase data.
- Cell Ranger — sourceCell Ranger is a set of analysis pipelines that process Chromium single-cell RNA-seq output to align reads, generate feature-barcode matrices and perform clustering and gene expression analysis (mkfastq, count, aggr, and reanalyze).
- gemBS — sourcegemBS is a high performance bioinformatic pipeline designed for highthroughput analysis of DNA methylation data from whole genome bisulfites sequencing data (WGBS). It combines GEM3, a high performance read aligner and bs_call, a high performance variant and methyation caller, into a streamlined and efficient pipeline for bisulfite sueqnce analysis.
- mountainClimber — sourcemountainClimber is a method for de novo identification of alternative transcript start sites and polyadenylation sites in RNA-seq dataSoftware type: transcript identification
- WashU Epigenome Browser — sourceThe WashU Epigenome Browser provides visualization, integration and analysis tools for epigenomic datasets. Since 2010, it has provided the scientific community with data from large consortia including the Roadmap Epigenomics and the ENCODE projects. Browser features include: (i) visualization using virtual reality (VR), which has implications in biology education and the study of 3D chromatin structure; (ii) expanded public data hubs, including data from the 4DN, ENCODE, Roadmap Epigenomics, TaRGET, IHEC and TCGA consortia; (iii) a more responsive user interface; (iv) a history of interactions, which enables undo and redo; (v) a feature we call Live Browsing, which allows multiple users to collaborate remotely on the same session; (vi) the ability to visualize local tracks and data hubs. Amazon Web Services also hosts the browser at https://epigenomegateway.org/.Software type: database, other
- Mediated Expression Score Regression (MESC) — sourceMESC is a method for quantifying genetic effects on disease mediated by assayed gene expression levels (Yao et al. 2020 Nat Genet).Software type: quantification
- Stratified LD fourth moments (S-LD4M) — sourceThis software implements our Stratified LD 4th moments regression (S-LD4M) method for estimating polygenicity across allele frequencies and functional categories, as described in our manuscript “Polygenicity of complex traits is explained by negative selection”.Software type: quantification
- Ascertained Sequentially Markovian Coalescent (ASMC) — sourceASMC is a method for inferring pairwise coalescence times implicating regions under negative selection that are enriched for disease heritability (Palamara et al. 2018 Nat Genet).Software type: other
- Signed LD profile (SLDP) regression — sourceSigned LD profile regression is a method for identifying genome-wide directional effects of signed functional annotations on diseases and complex traits, as described in our manuscript “Detecting genome-wide directional effects of transcription factor binding on polygenic disease risk”.Software type: other
- Vierstra digital genomic footprinting — sourcefootprint-tools is a python module for de novo detection of genomic footprints from DNase I data by simulating expected cleavage rates using a 6-mer DNase I cleavage preference model combined with density smoothing. Statistical significance of per-nucleotide cleavages are computed from a series emperically fit negative binomial distribution.
- Altius Index — sourceMethod for generating a master list / Index of DNaseI-Hypersensitive Sites ("consensus DHSs").
- Generate SIRV GTFs — sourceSet of scripts used to generate GTFs that include SIRV sequences for use with the ENCODE long read RNA-seq pipeline.Software type: other
- CrossStitch — sourceCrossStitch creates personalized reference-quality diploid genomes without de novo assembly. The basic idea is rather than trying to assemble a genome from scratch, it will leverage a reference genome as a baseline, and then update it with any SNPs, indels, or structural variations present in your sample. For the best results, the data requirements are similar to a de novo assembly: Illumina-based data for SNPs and Indels, Long Read data for structural variants, and Phasing data such as 10X Linked Reads and/or HiC data. However the CrossStitch process is much less demanding, produces more accurate results, and the process is much more predictable. The output will be a phased VCF file with all variants (SNPs, Indels, and SVs) as well as a phased personalized diploid genome including 2 copies of each chromosome with the variants inserted at the correct locations.
- Avocado — sourceAvocado is a multi-scale deep tensor factorization method for learning a latent representation of the human epigenome. The purpose of this model is two fold; first, to impute epigenomic experiments that have not yet been performed, and second, to learn a latest representation of the human epigenome that can be used as input for machine learning models in the place of epigenomic data itself.
- pbsv — sourcepbsv is a suite of tools to call and analyze structural variants in diploid genomes from PacBio single molecule real-time sequencing (SMRT) reads. The tools power the Structural Variant Calling analysis workflow in PacBio's SMRT Link GUI. pbsv calls insertions, deletions, inversions, duplications, and translocations. Both single-sample calling and joint (multi-sample) calling are provided.
- freebayes — sourcefreebayes is a Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs (single-nucleotide polymorphisms), indels (insertions and deletions), MNPs (multi-nucleotide polymorphisms), and complex events (composite insertion and substitution events) smaller than the length of a short-read sequencing alignment.
- TALON — sourceTALON is a program for identifying, quantifying, and filtering known and novel genes/isoforms in long read transcriptome data sets. It is technology-agnostic in that it works from mapped SAM files, allowing data from different sequencing platforms (i.e. PacBio and Oxford Nanopore) to be analyzed side by side.
- TranscriptClean — sourceTranscriptClean is a tool for variant-aware, reference-based error correction of long reads.
- RBNS Pipeline — sourceFrom Burge lab (Freese, P.): "The RBNS pipeline is a set of bioinformatics tools to analyze data from high-throughput sequencing experiments of protein-bound RNAs. The current version includes read splitting, calculation of kmer frequencies and enrichments, QC metrics, production of motif sequence logos, and RNA secondary structure analysis."Software type: other
- kallistokallisto is a program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. It is based on the novel idea of pseudoalignment for rapidly determining the compatibility of reads with targets, without the need for alignment. On benchmarks with standard RNA-Seq data, kallisto can quantify 30 million human reads in less than 3 minutes on a Mac desktop computer using only the read sequences and a transcriptome index that itself takes less than 10 minutes to build. Pseudoalignment of reads preserves the key information needed for quantification, and kallisto is therefore not only fast, but also as accurate than existing quantification tools. In fact, because the pseudoalignment procedure is robust to errors in the reads, in many benchmarks kallisto significantly outperforms existing tools.
- cWorld-Dekker — sourceA collection of perl/python/R scripts for manipulating 5C/Hi-C data, developed by Dekker lab.
- RSeQC — sourceRSeQC package provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. Some basic modules quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while RNA-seq specific modules evaluate sequencing saturation, mapped reads distribution, coverage uniformity, strand specificity, transcript level RNA integrity etc.Software type: filtering
- calcEnrich — sourceCalculate enrichment file using RT stop as foreground and base density as background
- Surrogate Variable Analysis — sourceThe sva package in Bioconductor contains functions for removing batch effects and other unwanted variation in high-throughput experiment.Software type: other
- Merge Peaks — sourceCWL-defined pipeline for using IDR to produce a set of peaks given two replicate eCLIP peaks
- juicertoolsSoftware package for analysis of Hi-C data.
- JuicerJuicer is a platform for analyzing high-resolution Hi-C data.
- dbGaP SRA to fastqConverts dbGaP-protected raw data in sra format to fastq format.
- JavaJava virtual machine
- PysamPython module warapping htslib C-API and samtools for accessing sam formatted alignment filesSoftware type: other
- dnase-densityGenerates normalized density signal from aligned and filtered reads for DNase ENCODE uniform processing pipeline.Software type: file format conversion
- dnase-qc-bamEvaluates a sample of paired or single-end aligned and filtered reads for DNase ENCODE uniform processing pipeline.Software type: quality metric
- bigWigAverageOverBed — sourceCompute average score of big wig over each bed, which may have introns.
- lrna-signalsSignal generation for bulk-RNA-seq ENCODE uniform processing pipeline.Software type: file format conversion
- MATS — sourceMATS is a computational tool to detect differential alternative splicing events from RNA-Seq data. The statistical model of MATS calculates the P-value and false discovery rate that the difference in the isoform ratio of a gene between two conditions exceeds a given user-defined threshold. From the RNA-Seq data, MATS can automatically detect and analyze alternative splicing events corresponding to all major types of alternative splicing patterns. MATS handles replicate RNA-Seq data from both paired and unpaired study design.
- Bowtie 2Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.
- rtracklayer — sourceExtensible framework for interacting with multiple genome browsers (currently UCSC built-in) and manipulating annotation tracks in various formats (currently GFF, BED, bedGraph, BED15, WIG, BigWig and 2bit built-in). The user may export/import tracks to/from the supported browsers, as well as query and modify the browser state, such as the current viewport.
- Genomic Alignments — sourceProvides efficient containers for storing and manipulating short genomic alignments (typically obtained by aligning short reads to a reference genome). This includes read counting, computing the coverage, junction detection, and working with the nucleotide content of the alignments.
- vcf2diploid — sourceCreates phased diploid genomes variants from a vcf file by integrating variants to a reference genome.Software type: variant annotation
- LongRangerLong Ranger is a set of analysis pipelines that processes Chromium sequencing output to align reads and call and phase SNPs, indels, and structural variants. These pipelines combine Chromium-specific algorithms with widely used components such as BWA, Freebayes, and GATK. Output is delivered in standard BAM, VCF, and BEDPE formats that are augmented with long range information.Software type: aligner, variant annotation
- chromCor.Rscript — sourceCalculates correlation between two replicate DNase signals.Software type: quality metric
- bigWigToWig — sourceThe binary bigWig format can be converted to the text based wig or bedGraph formats using this utility.Software type: file format conversion
- PyLiftover — sourcePyLiftover is a library for quick and easy conversion of genomic (point) coordinates between different assemblies. It uses the same logic and coordinate conversion mappings as the UCSC liftOver tool.Software type: other
- BitSeq — sourceThe BitSeq package is targeted for transcript expression analysis and differential expression analysis of RNA-seq data in two stage process. In the first stage it uses Bayesian inference methodology to infer expression of individual transcripts from individual RNA-seq experiments. The second stage of BitSeq embraces the differential expression analysis of transcript expression. Providing expression estimates from replicates of multiple conditions, Log-Normal model of the estimates is used for inferring the condition mean transcript expression and ranking the transcripts based on the likelihood of differential expression.
- windowTrimmer — sourceThis script is intended to crawl through bed files to filter out reads that are too concentrated within a specified base-pair window.
- dnase-index-bwa — sourceIndexes the reference genome by BWA, and processes mappability and exclusion list (previously "blacklist") for DNase ENCODE uniform processing pipeline.Software type: other
- dnase-rep-corr — sourceCalculated correlation beteen two replicate signals for DNase ENCODE uniform processing pipeline.Software type: quality metric
- dnase-call-hotspots — sourceCalls hotspots and peaks on filtered alignments by hotspot2 for DNase ENCODE uniform processing pipeline.Software type: peak caller
- dnase-eval-bam — sourceEvaluates a sample of paired or single-end aligned and filtered reads for DNase ENCODE uniform processing pipeline.Software type: quality metric
- dnase-filter-se — sourceMerges and filters single-end aligned reads for DNase ENCODE uniform processing pipeline.Software type: filtering
- dnase-filter-pe — sourceMerges and filters paired-end aligned reads for quality and UMI duplicates for DNase ENCODE uniform processing pipeline.Software type: filtering
- dnase-align-bwa-se — sourceAligns single-end reads by BWA for DNase ENCODE uniform processing pipeline.Software type: aligner
- dnase-align-bwa-pe — sourceAligns paired-end reads by BWA for DNase ENCODE uniform processing pipeline.Software type: aligner
- DNase Pipeline — sourceRepository for Uniform processing of DNase Hypersensitivity (DNaseHS) and Digital Genomic Footprinting (DGF) though pipelines as implemented by the ENCODE DCC.