Showing 13 of 13 results

• Software

  released

  dnase-align-bwa-pe — source

  Aligns paired-end reads by BWA for DNase ENCODE uniform processing pipeline.

  Software type: aligner

• Software

  released

  dnase-align-bwa-se — source

  Aligns single-end reads by BWA for DNase ENCODE uniform processing pipeline.

  Software type: aligner

• Software

  released

  LongRanger

  Long 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, Fre

  Software type: aligner, variant annotation

• Software

  released

  lrna-align-tophat-se — source

  Aligns single-end reads by TopHat for long-RNA-seq ENCODE uniform processing pipeline.

  Software type: aligner

• Software

  released

  lrna-align-star-pe — source

  Aligns paired-end reads by STAR for long-RNA-seq ENCODE uniform processing pipeline.

  Software type: aligner

• Software

  released

  NextGenMap — source

  NextGenMap 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

• Software

  released

  rampage-align — source

  Aligns paired-end reads by STAR for Rampage ENCODE uniform processing pipeline.

  Software type: aligner

• Software

  released

  lrna-align-star-se — source

  Aligns single-end reads by STAR for long-RNA-seq ENCODE uniform processing pipeline.

  Software type: aligner

• Software

  released

  srna-align — source

  Aligns single-end reads by STAR for small-RNA-seq ENCODE uniform processing pipeline.

  Software type: aligner

• Software

  released

  lrna-align-tophat-pe — source

  Aligns paired-end reads by TopHat for long-RNA-seq ENCODE uniform processing pipeline.

  Software type: aligner

• Software

  released

  STAR — source

  STAR (Spliced Transcript Alignment to a Reference) aligns short and long RNA-seq reads to a reference genome using uncompressed suffix arrays.

  Software type: aligner

• Software

  released

  BWA — source

  BWA 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: 2008050

  Software type: aligner

• Software

  released

  TopHat — source

  Fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons.

  Software type: aligner