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v1.0.0 beta3

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@blahah blahah released this 23 Feb 11:03
· 124 commits to master since this release
v1.0.0.beta3
574f08e

screenshot 2014-10-17 11 22 27

transrate v1.0.0 beta 3

This is the third 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/.

Installation

Simple install

This is the simplest option if you just want to use transrate from the command-line...

Download one of the binaries linked below, unpack it, and add it to your PATH.

Advanced/developer install

This is the option you need if you want to develop code that uses transrate as a library...

$ gem install --pre transrate --version 1.0.0.beta3
$ transrate --install-deps

Changes

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

Changelog

beta3

  • Transrate will automatically choose the optimal set of contigs from an assembly, maximising both the quality of the contigs and the proportion of the read evidence that is used. It now reports the raw assembly score as well as the optimised assembly score. The optimal assembly is found in good.*.fa
  • Transrate can now merge assemblies with the --merge-assemblies command, choosing the optimal set of contigs from all the input assemblies
  • Some great improvements to Salmon have been included in this release
  • Transrate now estimates the insert size distribution from the reads
  • Transrate is now distributed as a binary package (available for linux 64bit, and osx). This should greatly simplify installation for most users.

beta2

  • 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
  • Users, especially Matt Macmanes, for diligent testing and bug reporting
  • The SNAP team for responding rapidly to our bug reports
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