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