v1.0.0 beta 2

transrate v1.0.0 beta 2

This is the second beta release of transrate v1. Please report any bugs on the issue tracker. Documentation for this release is on the transrate website: http://hibberdlab.com/transrate/.

To install:

$ gem install --pre transrate --version 1.0.0.beta2
$ transrate --install-deps

If you are updating from a version below v1, please see the release notes for v1.0.0.alpha1.

Changelog

There are major updates in this beta:

• We have moved to using Salmon for read assignment. This has brought a massive speedup over using eXpress, because Salmon can use any number of cores (while eXpress is restricted to 3), and Salmon is generally optimised for speed
• We've managed to eliminate much of the IO bottleneck that was caused by processing BAM files, thanks to the collaboration of the Salmon developer
• We've fixed some bugs in the SNAP aligner that we depend on
• Minor bug fixes in basic contig metrics for unusual kinds of inputs
• Improved error handling and logging
• Improved dependency management, with fewer dependencies

Acknowledgements

• Rob Patro, developer of Salmon, for his hard work on making Salmon work well with transrate
• The SNAP team for responding rapidly to our bug reports