ENCODE Software
All software used or developed by the ENCODE Consortium
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- 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.
- 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.
- 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.
- interpretation_samples — sourceInterpretation code for Segway samples that produces classifier output and diagnostic plots from the apply_samples.py, for test samples.Software type: genome segmentation
- 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
- liftOverThis UCSC tool converts genome coordinates and genome annotation files between assemblies.
- fastq-tools — sourceA collection of small and efficient programs for performing some common and uncommon tasks with FASTQ files.Software type: other
- 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).
- 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.
- PysamPython module warapping htslib C-API and samtools for accessing sam formatted alignment filesSoftware type: other
- 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.
- 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