ENCODE Software
All software used or developed by the ENCODE Consortium
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- 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
- 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
- trim-adapters-illumina — sourceThis program will trim adapters from pair-end sequencing tags produced using the Illumina(c) platform.Software type: filtering
- StamPipesThis is a focused collection of makefiles and scripts to for analysis on Illumina sample data. While this probably can't be directly used by someone not in our lab, it might be a useful reference for others.Software type: filtering
- edwBamFilter — sourceRemove reads from a BAM file based on a number of criteriaSoftware type: filtering
- Trim Galore — sourceTrim Galore! is a wrapper script to automate quality and adapter trimming as well as quality control, with some added functionality to remove biased methylation positions for RRBS sequence files (for directional, non-directional (or paired-end) sequencing).Software type: filtering
- Picard — sourceA set of tools (in Java) for working with next generation high-throughput sequencing (HTS) data in the BAM format. Picard is implemented using the HTSJDK Java library HTSJDK, supporting accessing of common file formats, such as SAM and VCF, used for high-throughput sequencing data. Currenty no published paper for Picard software.Software type: filtering, other
- Phantompeakqualtools — sourceUsed to generate these quality metrics: NSC and RSC. The NSC (Normalized strand cross-correlation) and RSC (relative strand cross-correlation) metrics use cross-correlation of stranded read density profiles to measure enrichment independently of peak calling.Software type: quality metric, filtering
- Irreproducible Discovery Rate (IDR) — sourceMeasures consistency between replicates in high-throughput experiments. Also uses reproducibility in score rankings between peaks in each replicate to determine an optimal cutoff for significance. The core IDR R package can be downloaded from the IDR download page: http://cran.r-project.org/web/packages/idr/index.htmlSoftware type: quality metric, filtering