bicycle bicycle

Downloads

bicycle v1.8.2 downloads
binary downloads
bicycle 1.8.2 Download and uncompress it. Please, refer to manual to learn how to use bicycle. This ver requires:

  • Operating system: Linux/OSX.
  • Java 1.8 or higher.
  • One of the following aligners:
    • bowtie1 0.12.7 or higher and 1.0.0 or lower.
    • bowtie2 aligner 2.3.2 or higher.
  • samtools 0.1.8 or higher.
 
Ubuntu 14.04 LiveCD
LiveCD 14.04 Ubuntu Linux 64bit OS with bicycle 1.8.0 installed along with other popular tools for whole genome bisulfite sequencing data analysis. See this page for more details.
 
Docker image
Go to Dockerhub or pull it by running 'docker pull singgroup/bicycle'. To run the image in Windows, have a look at this tutorial.
 
Source code is available at the official GitHub's repository.
Sample data
Quickstart sample data
Simulated data Uncompress the zip file. There are two directories: one for the reference genome and one with reads in one sample.
The simulated data was generated with Sherman and contains reads from a subset of the chr1 of Mus musculus genome (mm9) and the Ecoli genome (to estimate bisulfite conversion and alignment error).
The methylation level in mm9 is CG: 30%, CH: 5%. The bisulfite conversion rate in Ecoli is 99.9%. All reads are pooled in the same sample (sample-1 subdirectory inside the reads directory).
Case study data
Raw data A public dataset from this paper from Bernstein et al. 2015 that describes a new targeted bisulfite sequencing approach is used. This dataset consists of five non-diabetic and five type 2 diabetic samples from human pancreatic islets that were sequenced with an Illumina Miseq sequencer (14.15 million of 150 base pair paired-end reads).
Reference genome The reference genome along with its corresponding bowtie 2 indexes to use in the case study.
Target regions The target regions of interest to use in the case study.

Version history (downloads for old releases are availble here)

v1.8.2 (25.04.2020)
  • Fixes bug when splitting fastq files during alignment.
v1.8.1 (11.06.2018)
  • Fixes cytosines context calculation.
v1.8.0 (8.10.2017)
  • Add support for Bowtie 2.
  • Adds parameter --onlyWithOneAlignment in methylation analysis.
  • Adds a report in the .summary file containing the number of reads filtered by each filter in methylation analysis.
  • Shows logs of bowtie-build during bicycle reference-index
  • Marks as ambiguous reads in non-directional alignments where the read aligns both in directional and non-directional
  • Adds support for adding JVM parameters in bicycle launch command
  • Bug fixes.
v1.7.2 (31.5.2017)
  • Fixes bug of empty *.methylation files in some environments (e.g. Docker in Windows).
  • Fixes creation of strange empty dir in output directory.
v1.7.1 (13.5.2017)
  • Fixes bug during alignment (IOException: Invalid Argument).
v1.7.0 (10.5.2017)
  • Makes samtools and bowtie directories optional.
  • Adds Dockerfile for creating docker images.
v1.6.0 (5.5.2017)
  • Adds context parameter on differential methylation analysis.
  • Improves logging messages.
  • Bug fixes.
v1.5.0 (21.07.2016)
  • Added support for non-directional protocol in both paired and single end.
  • Differential Mehtylation Analysis.
  • Migration of source code to Maven and Git.
v1.1.0 (27.07.2012)
  • Added support for paired-end.