v1.6.2

Hotfix release to fix paired-end / single-end read detection.

v1.6.1

Minor bugfixes improving paired-end vs single-end detection and error handling. The requirement to specify bowtie2 indices when using BAM files has been removed.

v1.6

Adds automatic experiment and replicate grouping and processing, automatic detection and processing of PE and SE sequencing reads, ability to set a separate data directory, dry-run capabilities to check groupings, plus some minor bugfixes, refactoring and under-the-hood changes.

v1.5.3

This release adds improved handling of paired-end data, improved handling of read coverage in RPM (reads per million reads) as standard, ability to write coverage bedGraph files, the ability to use completely custom normalisation routines, the ability to handle ChIP-seq data, and additional under-the-hood improvements.

v1.4.6

This release added support for paired end sequencing to the pipeline. Formally tagging this version before the next release, which brings in some code refactoring and new features.

v1.4

A number of important changes in this release, including a more accurate read extension method. Some defaults have changed, including the file output format which is now set as bedgraph.

v1.2

Major changes from v1.0, including a more accurate normalisation method, the ability to process BAM files directly and much better file handling. Sample names can be taken directly from the file names (an "index.txt" file is no longer required, but can still be used if desired). The requirement for bedtools has been dropped, and memory usage is much lower. See the changelog for more details.

Initial release

Initial release