ENCODE Software
All software used or developed by the ENCODE Consortium
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- 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.
- 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.
- dbGaP SRA to fastqConverts dbGaP-protected raw data in sra format to fastq format.
- 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
- lrna-signalsSignal generation for bulk-RNA-seq ENCODE uniform processing pipeline.Software type: file format conversion
- 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.
- rampage-mad-qc — sourceMean Absolute Deviation (MAD) and correlation calculated from two replicates for Rampage ENCODE uniform processing pipeline.Software type: quality metric
- srna-mad-qc — sourceMean Absolute Deviation (MAD) and correlation calculated from two replicates for small-RNA-seq ENCODE uniform processing pipeline.Software type: quality metric
- lrna-mad-qc — sourceMean Absolute Deviation (MAD) and correlation calculated from two replicates for bulk-RNA-seq ENCODE uniform processing pipeline.Software type: quality metric
- rampage-idr — sourceIrreproducible Discovery Rate (IDR) calculation from two replicates for Rampage ENCODE uniform processing pipeline.Software type: quality metric
- rampage-peaks — sourcePeak calling by GRIT for Rampage ENCODE uniform processing pipeline.Software type: peak caller
- lrna-quantification — sourceQuantification of annotation results by RSEM for bulk-RNA-seq ENCODE uniform processing pipeline.Software type: transcript identification
- rampage-signals — sourceSignal generation for Rampage ENCODE uniform processing pipeline.Software type: file format conversion
- srna-signals — sourceSignal generation for small-RNA-seq ENCODE uniform processing pipeline.Software type: file format conversion
- lrna-signals-unstranded — sourceSignal generation from unstranded alignments for bulk-RNA-seq ENCODE uniform processing pipeline.Software type: file format conversion
- lrna-signals-stranded — sourceSignal generation from stranded alignments for bulk-RNA-seq ENCODE uniform processing pipeline.Software type: file format conversion
- rampage-align — sourceAligns paired-end reads by STAR for Rampage ENCODE uniform processing pipeline.Software type: aligner
- srna-align — sourceAligns single-end reads by STAR for small-RNA-seq ENCODE uniform processing pipeline.Software type: aligner
- lrna-align-tophat-se — sourceAligns single-end reads by TopHat for bulk-RNA-seq ENCODE uniform processing pipeline.Software type: aligner
- lrna-align-tophat-pe — sourceAligns paired-end reads by TopHat for bulk-RNA-seq ENCODE uniform processing pipeline.Software type: aligner
- lrna-align-star-se — sourceAligns single-end reads by STAR for bulk-RNA-seq ENCODE uniform processing pipeline.Software type: aligner
- lrna-align-star-pe — sourceAligns paired-end reads by STAR for bulk-RNA-seq ENCODE uniform processing pipeline.Software type: aligner
- srna-index-star — sourceIndexing of reference genome by STAR for small-RNA-seq ECODE uniform processing pipeline.Software type: other
- lrna-index-tophat — sourceIndexing of reference genome by TopHat for bulk-RNA-seq ECODE uniform processing pipeline.Software type: other
- lrna-index-star — sourceIndexing of reference genome by STAR for bulk-RNA-seq ENCODE uniform processing pipeline.
- lrna-index-rsem — sourceIndexing of reference genome by RSEM for bulk-RNA-seq ECODE uniform processing pipeline.
- RNA pipelines — sourceRepository of all RNA-seq (long-, small-, and rampage) ENCODE Uniform processing pipelines.
- dme-extract-pe — sourceExtracts DNA-methylation from WGBS paired-end alignments for ENCODE uniform processing pipeline.
- dme-align-pe — sourceAlignment by bowtie2 for paired-end WGBS (dna-methylation) experiments for ENCODE uniform processing pipeline
- dme-index-bismark-bowtie2 — sourceIndexes reference (and lambda) genomes using bismark and bowtie2, creating an archive file need for WGBS dna-methylation mapping of the ENCODE uniform processing pipeline.
- dme-rep-corr — sourceCorrelates two WGBS replicate CpG methylation results for ENCODE uniform processing pipeline.
- dme-bg-to-signal — sourceConverts WGBS Bismark generated bedGraphs to bigWig format signal files for ENCODE uniform processing pipeline.
- dme-cx-to-bed — sourceConverts WGBS Bismark context report to bed and bigBed file formats for ENCODE uniform processing pipeline.
- dme-extract-se — sourceExtracts DNA-methylation from WGBS single-end alignments for ENCODE uniform processing pipeline.
- dme-align-se-parallel — sourceAlignment by bowtie1 for single-end WGBS (dna-methylation) experiments for ENCODE uniform processing pipeline
- dme-index-bismark — sourceIndexes reference (and lambda) genomes using bismark and bowtie1, creating an archive file need for WGBS dna-methylation mapping for the ENCODE uniform processing pipeline.
- DNA-me pipeline — sourceThis is the git repository for all DNA methylation (WGBS) uniform pipeline code dun on dnanexus by the ENCODE DCC.Software type: other