Showing 19 of 19 results

• Software

  released

  PyLiftover — source

  PyLiftover 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

• Software

  released

  WGBS output processor — source

  Convert a Bismark CX_report file to bed-like files

  Software type: other

• Software

  released

  srna-index-star — source

  Indexing of reference genome by STAR for small-RNA-seq ECODE uniform processing pipeline.

  Software type: other

• Software

  released

  lrna-index-tophat — source

  Indexing of reference genome by TopHat for long-RNA-seq ECODE uniform processing pipeline.

  Software type: other

• Software

  released

  nsolver — source

  Normalization of Nanostring array counts

  Software type: other

• Software

  released

  Concat-fastq — source

  Concat-fastqs is an applet available for DNA-nexus to concatenate a set of fastqs that should be merged for analysis.

  Software type: other

• Software

  released

  gnuplot — source

  Gnuplot is a portable command-line driven graphing utility for Linux, OS/2, MS Windows, OSX, VMS, and many other platforms. The source code is copyrighted but freely distributed (i.e., you don't have to pay for it). It was originally created to allow scie

  Software type: other

• Software

  released

  cutadapt — source

  Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.

  Software type: other

• Software

  released

  Tophat BAM Repair — source

  tophat_bam_xsA_tag_fix.pl was written by x wei to allow the use of tophat 2.0.8 in the ENCODE pipelines. It reads a bam file generated from paired-ended fastqs by tophat 2.0.8 and corrects the XS:A:+ or XS:A:- tags showing read strandedness.

  Software type: other

• Software

  released

  Preseq — source

  From the Smith lab: "The preseq package is aimed at predicting and estimating the complexity of a genomic sequencing library, equivalent to predicting and estimating the number of redundant reads from a given sequencing depth and how many will be expected

  Software type: other

• Software

  released

  DNA-me pipeline — source

  This is the git repository for all DNA methylation (WGBS) uniform pipeline code dun on dnanexus by the ENCODE DCC.

  Software type: other

• Software

  released

  Picard — source

  A 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

  Software type: filtering, other

• Software

  released

  Bismark — source

  A tool to map bisulfite converted sequence reads and determine cytosine methylation states. The output produced by Bismark discriminates between cytosines in CpG, CHG and CHH context and enables bench scientists to visualize and interpret their methylati

  Software type: other

• Software

  released

  Makepseudoreplicates

  Generate psuedoreplicates for self-consistency tests.

  Software type: other

• Software

  released

  dnase-index-bwa — source

  Indexes the reference genome by BWA, and processes mappability and blacklist for DNase ENCODE uniform processing pipeline.

  Software type: other

• Software

  released

  snow — source

  The snow package provides support for simple parallel computing on a network of workstations using R. A master R process calls makeCluster to start a cluster of worker processes; the master process then uses functions such as clusterCall and clusterApply

  Software type: other

• Software

  released

  SeparateReadpairs — source

  Splits up the interleaved file into two valid paired fastqs.

  Software type: other

• Software

  released

  Samtools — source

  Samtools is a suite of programs for interacting with high-throughput sequencing data. SAMtools implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides univers

  Software type: other

• Software

  released

  Pysam

  Python module warapping htslib C-API and samtools for accessing sam formatted alignment files

  Software type: other