transrate v1.0.3

transrate v1.0.3

This is is a patch release of transrate v1, to accompany the publication of our paper about transrate.

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.

• Linux 64 bit: transrate-1.0.3-linux-x86_64.tar.gz
• OSX: transrate-1.0.3-osx.tar.gz

Download the example data so you can test your installation has worked.

Advanced/developer install

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

$ gem install transrate
$ transrate --install-deps all

Changes

• Output additional columns with names that match the quality score components in the paper
• Make --install-deps messages clearer (fixes #187)
• Track working directory on the package loading script (#fixes #186)
• Updated SNAP dependency to v1.0dev96
• Updated Salmon dependency to v0.6.0
• Check for duplicate paths in input
• Remove some ancient contig metrics that were deprecated
• Updated the packaging process to be more robust
• Log commands used to shell out when --loglevel is debug
• Automatically increase SNAP locationSize parameter if it fails (thanks to @jorvis)

For changelog history before v1.0.0, please see the release notes for v1.0.0 final.

Known issues

• There is a SNAP bug that causes a random subset of reads not to be processed about one in ten times SNAP is run. This only affects OSX, and we are working with the SNAP developers to find a fix. Linux users should not be affected.

v1.0.2

transrate v1.0.2

This is is a patch release of transrate v1, including some small changes to help messages and documentation, as well as some new features requested by reviewers.

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.

• Linux 64 bit: transrate-1.0.2-linux-x86_64.tar.gz
• OSX: transrate-1.0.2-osx.tar.gz

Download the example data so you can test your installation has worked.

Advanced/developer install

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

$ gem install transrate
$ transrate --install-deps

Changes

• new feature: transrate outputs one file per contig metric (see http://hibberdlab.com/transrate/metrics.html) containing the contigs that performed poorly on that metric alone. These can potentially be used or fixed by the user. Requested by an anonymous reviewer.
• new feature: an expression-weighted assembly score as an alternative to the transrate score. Requested by an anonymous reviewer.
• fix documentation issues #179, #164 and #165 (thanks @macmanes and @ctb)

For changelog history before v1.0.0, please see the release notes for v1.0.0 final.

v1.0.1

transrate v1.0.1

This is the final release of transrate v1. This our first stable production release. 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.

• Linux 64 bit: transrate-1.0.1-linux-x86_64.tar.gz
• OSX: transrate-1.0.1-osx.tar.gz

Download the example data so you can test your installation has worked.

Advanced/developer install

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

$ gem install transrate
$ transrate --install-deps

Changes

• fixed an issue where providing multiple assemblies would break reference-based mode
• refactored the command-line so that all CLI code can be unit tested
• tidied up command-line output so that a neat directory structure is created
• the colourful banner is now only shown when the terminal is wide enough
• the packaged binary version no longer lists the option to install read dependencies, as they are pre-packaged
• made error message more helpful for the case where Trinity's FASTA headers cause problems
• documented the ability to take multiple FASTQ files in the CLI --help
• all SNAP logs (stdout and stderr) are now saved to the logs directory

For changelog history before v1.0.0, please see the release notes for v1.0.0 final.

v1.0.0 final

transrate v1.0.0 final

This is the final release of transrate v1. This our first stable production release. 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.

• Linux 64 bit: transrate-1.0.0-linux-x86_64.tar.gz
• OSX: transrate-1.0.0-osx.tar.gz

Download the example data so you can test your installation has worked.

Advanced/developer install

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

$ gem install transrate
$ transrate --install-deps

Changes

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

Changelog

v1.0.0 final

• All metrics are now reported to an appropriate number of significant figures
• Our dependency on SNAP has been updated to v1.0beta.18 after they incorporated bug fixes we submitted
• Our dependency on Salmon has been updated to v0.4.2 to include some bug fixes
• The command-line interface has been cleaned up and simplified
• A bug with dynamic loading of C extensions, introduced in a previous commit, has been fixed

beta4

• We've updated our Salmon dependency to v0.4.0, which brings an awesome speed increase, especially for small datasets, as well as some improvement in accuracy for our read metrics.
• Fixed a bug in --install-deps where it would always try to install all the dependencies
• Improved handling of FASTA input edge-cases and unusual formatting
• Better handling and reporting of errors and crashes in the dependencies
• A big improvement to reference-based metrics when comparing to a reference that has repetitive sequences. Users should now see considerably higher reference coverage in some places (before, BLAST was masking out repetitive regions). Thanks to Nick Schurch and Chris Cole at Dundee for their analysis that led to discovering this issue.
• Some command-line arguments have been reordered and their short-names changed, so now --right has -r for short and --reference has -a for short. Thanks to Matt Macmanes for highlighting this.

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

v1.0.0 beta4

transrate v1.0.0 beta 4

This is the fourth 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.

• Linux 64 bit: transrate-1.0.0.beta4-linux-x86_64.tar.gz
• OSX: transrate-1.0.0.beta4-osx.tar.gz

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.beta4
$ transrate --install-deps

Changes

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

Changelog

beta4

• We've updated our Salmon dependency to v0.4.0, which brings an awesome speed increase, especially for small datasets, as well as some improvement in accuracy for our read metrics.
• Fixed a bug in --install-deps where it would always try to install all the dependencies
• Improved handling of FASTA input edge-cases and unusual formatting
• Better handling and reporting of errors and crashes in the dependencies
• A big improvement to reference-based metrics when comparing to a reference that has repetitive sequences. Users should now see considerably higher reference coverage in some places (before, BLAST was masking out repetitive regions). Thanks to Nick Schurch and Chris Cole at Dundee for their analysis that led to discovering this issue.
• Some command-line arguments have been reordered and their short-names changed, so now --right has -r for short and --reference has -a for short. Thanks to Matt Macmanes for highlighting this.

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

v1.0.0 beta3

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.

• Linux 64 bit: transrate-1.0.0.beta3-linux-x86_64.tar.gz
• OSX: transrate-1.0.0.beta3-osx.tar.gz

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

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

v1.0.0 beta 1

transrate v1.0.0 beta 1

This is the first 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.beta1
$ transrate --install-deps

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

Changelog

• depend on SNAP dev build 63, which includes a variety of fixes for bugs found by @cboursnell. The SNAP team have been extremely helpful by rapidly responding to all our reports.
• the contig score no longer includes the 'uniqueness' component, because tests showed it was penalising valid alternative isoforms.
• contigs are automatically sorted into FASTA files containing the 'good', 'fragmented', 'chimeric' and 'bad' contigs.

v1.0.0 alpha 3

transrate v1.0.0 alpha 3

This is the third alpha release of transrate v1.

To install:

$ gem install --pre transrate --version 1.0.0.alpha3
$ transrate --install-deps

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

Changelog

Some minor changes and bug-fixes:

• avoid re-running stages of the read-processing if their output files already exist
• add timestamp to logger #94
• print help message when transrate is run with no arguments #93
• transrate now reports the version number for missing dependencies
• fix samtools sort threads argument #96
• help message updated to include transrate score example and both authors
• updated coverage calculation
• fix a segfault in bam-read (cboursnell/transrate-tools@8fec0e9, #98)

v1.0.0 alpha 2

transrate v1.0.0 alpha 2

This is the second alpha release of transrate v1.

To install:

$ gem install --pre transrate --version 1.0.0.alpha2
$ transrate --install-deps

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

Changelog

Small changes and bug fixes:

• show full errors when dependency installation fails
• include expression in read metrics
• fix problem where some contigs showed 'NA' for score and other read-based metrics
• include expression in read metrics