ENCODE Software
All software used or developed by the ENCODE Consortium
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- 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
- 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
- NextGenMap — sourceNextGenMap is a flexible and fast read mapping program that is more than twice as fast as BWA while achieving a mapping sensitivity similar to Stampy.Software type: aligner
- 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
- BWA — sourceBWA is a software package for mapping low-divergent sequences based on a Burrows-Wheeler index against a large reference genome, such as the human genome. Publications for the short read alignment component is found at PMID: 19451168, while PMID: 20080505 outlines the algorithm to align sequences >200bp up to 1Mb.Software type: aligner
- WASP — sourceWASP is a software package for two related tasks: (1) correcting allelic bias in mapped sequencing reads and, (2) identifying molecular quantitative trait loci (QTLs) using next-generation sequencing data (e.g. gene expression QTLs or histone mark QTLs). The WASP mapper works with any read mapping pipeline that outputs BAM or SAM format. WASP identifies molecular QTLs using a statistical test that combines information about the total depth and allelic imbalance of mapped reads. WASP can call QTLs with very small sample sizes (as few as 10) compared to traditional QTL mapping approaches.Software type: aligner, variant annotation