capcruncher 0.2.2

An end-to-end solution for processing Capture-C, Tri-C and Tiled-C data

CapCruncher

Analysis software for Capture-C, Tri-C and Tiled-C data.

CapCruncher is a tool designed to automate the processing of Capture-C, Tri-C and Tiled-C data from FASTQ files, the package is written in python and consists of an end-to-end data processing pipline together with a supporting command line interface to enable finer grained control. The pipeline provided is fast, robust and scales from a laptop to a computational cluster.

For further information see the documentation

Changelog

CapCruncher v0.2.2 (2022-03-03)

Bug Fixes

• alignment filtering: Prevent cluster errors due to lack of allocated memory. (#153) (c77c2fd), closes #149 #150 #143 #152 #151
• alignment filtering: Enabled max memory adjustment for alignment filtering (#156) (05daf2d)
• packaging: Fix issue with missing report text file (#157) (b172c8b)
• pipeline: Fix dask client shutdown related errors (#154) (80f1f1b)
• report: Fixes error when generating a report for a single sample(#149) (3509c7c)

Features

• alignment annotation: Enabled biasing of duplicate removal towards trans reporters (#151) (2de4e35). This effetively increases the proportion of cis interactions in comparison to trans.
• preprocessing: Reduced disk space required by fastq files (#150) (b43dff2)
• reporters compare: Improved the utility of the reporters-compare CLI (#145) (be0b8b0)
• utilities: Added CLI utility ti get viewpoint coordinates from capture oligos (#144) (a7ffcaf)