Canu v1.4

@brianwalenz brianwalenz released this Dec 13, 2016 · 112 commits to master since this release

These are release notes for Canu version 1.4, which was released on December 13, 2016. Canu is specialized for assembly of single-molecule high-noise sequences. Full documentation can be found at http://canu.readthedocs.org/.

This release provides a stable, tested, and documented version of the software. The binary distributions should work on any relatively recent version of the respective OS. The source code distribution contains everything you need (even the Perl modules!) to create a binary distribution for your own specific OS.

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Minimum Requirements

  • Perl 5.12.0, or File::Path 2.08
  • Java SE 8
  • GCC 4.5 (for compilation only)
  • OS X 10.10 (for binaries only)
  • Gnuplot (optional, for generating diagnostic graphs)

Installation

Users can download Canu as source code or as pre-compiled binaries. The source code package needs to be compiled and installed before it can be used. The binary distributions need only be unpacked, but they are not available for all platforms.

To install from source code:

gunzip -dc v1.4.tar.gz |tar -xf -
cd canu-1.4/src
make -j8
cd ..

To install from a binary distribution:

xz -dc canu-1.4.*.tar.xz |tar -xf -

In both cases, canu is installed directory in canu-1.4/-, for example, canu-1.4/Linux-amd64. You can run the assembler with:

canu-1.4/*/bin/canu

Changes

  • Removed dependency on Filesys::Df.
  • Reduced size of overlap stores by 33 1/3%.
  • Added inline Snappy compression overlaps, instead of a separate gzip process. This greatly reduces resources required for building large overlap stores.
  • Memory mapped files are no longer used. Performance on distributed file systems should be improved. Virtual memory usage is greatly reduced.
  • Fixed a variety of issues in GFA output on unitigs, and added GFA output on contigs.
  • Added options onSuccess and onFailure to run a command when Canu terminates successfully or fails unexpectedly.
  • Added support for PBSPro.
  • Fixed the usual assortment of random bugs.
  • Added other minor improvements.

Known Issues

See the issues page for up-to date open issues. The currently known issues are:

  • For AT/GC rich eukaryotic genomes, it is beneficial to increase the filtering stringency over the default. Specifying corMaxEvidenceErate=0.15 (from the default of 0.2) is generally sufficient.
  • As a computational optimization, you can decrease the error rate (errorRate=0.013), especially for inbred strains, on Oxford Nanopore R9 2D data and high-coverage P6 PacBio data.
  • LSF support has limited testing
  • Large memory usage while unitig consensus calling on unitigs over 100MB in size (140Mb contig uses approximate 75GB).
  • Bubbles are not captured in the contig graph, but are included in the unitig graph. No attempt at marking bubbles is made.

Legal

As Canu is derived from the Celera Assembler, most of the code is GPL licensed. This distribution includes code from Boost, pbdagcon, pbutgcns, and Falcon. For a copyright summary see the README.licenses file as well as individual component licenses included in the repository (boost, falcon, pbdagcon). For more details, see the header in each source file which details its history.

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Canu v1.3

@skoren skoren released this May 31, 2016

These are release notes for Canu version 1.3, which was released on June 8, 2016. Canu is specialized for assembly of single-molecule high-noise sequences. Full documentation can be found at http://canu.readthedocs.org/.

This release provides a stable, tested, and documented version of the software. The binary distributions should work on any relatively recent version of the respective OS. The source code distribution contains everything you need (even the Perl modules!) to create a binary distribution for your own specific OS.

Citation

Installation

Requirements

  • Java SE 8 +
  • GCC 4.5+ (for compilation only)
  • Filesys::Df Perl module (for binaries only, depending on perl version)
  • OS X 10.10 or newer (for binaries only)
  • Gnuplot (optional for generating HTML graphs)

Users can download Canu as source code or as pre-compiled binaries. The source code package needs to be compiled and installed before it can be used. The binary distributions need only be unpacked, but they are not available for all platforms.

To install from source code:

gzip -dc canu-1.3.tar.gz | tar -xf -
cd canu-1.3/src
make -j8
cd ..

To install from a binary distribution:

bzip2 -dc canu-1.3*.tar.bz2 | tar -xf -

In both cases, canu is installed directory in canu-1.3/-, for example, canu-1.3/Linux-amd64. You can run the assembler with:

canu-1.3/*/bin/canu

Changes

  • Rewritten bogart algorithm to auto-set error rate and avoid false-breaks due to repeats.
  • Updated GFA output to include all edges in the graph.
  • Updated MHAP release to 2.1 for further speed improvements and improved repeat suppression.
  • Auto-set MHAP and other parameters based on genome coverage.
  • Fix slow 3-overlapErrorAdjustment runtime.
  • Fix memory request for 3-overlapErrorAdjustment.
  • Pipeline bug fixes

Known Issues

See the issues page for up-to date open issues. The currently known issues are:

  • For AT/GC rich eukaryotic genomes, it is beneficial to increase the filtering stringency over the default. Specifying corMaxEvidenceErate=0.15 (from the default of 0.2) is generally sufficient.
  • As a computational optimization, you can decrease the error rate (errorRate=0.013), especially for inbred strains, on Oxford Nanopore R9 2D data and high-coverage P6 PacBio data.
  • LSF support has limited testing
  • Large memory usage while unitig consensus calling on unitigs over 100MB in size (140Mb contig uses approximate 75GB).
  • Distributed file systems (such as GPFS) causes issues with memory mapped files, slowing down parts of Canu, including meryl (0-mercounts) and falcon-sense (2-correction).

Legal

As Canu is derived from the Celera Assembler, most of the code is GPL licensed. This distribution includes code from Boost, pbdagcon, pbutgcns, and Falcon. For a copyright summary see the README.licenses file as well as individual component licenses included in the repository (boost, falcon, pbdagcon). For more details, see the header in each source file which details its history.

Downloads

Canu v1.2

@skoren skoren released this Mar 31, 2016 · 705 commits to master since this release

These are release notes for Canu version 1.2, which was released on April 7, 2016. Canu is specialized for assembly of single-molecule high-noise sequences. Full documentation can be found at http://canu.readthedocs.org/.

This release provides a stable, tested, and documented version of the software. The binary distributions should work on any relatively recent version of the respective OS. The source code distribution contains everything you need (even the Perl modules!) to create a binary distribution for your own specific OS.

Citation

Installation

Requirements

  • Java SE 8 +
  • GCC 4.5+ (for compilation only)

Users can download Canu as source code or as pre-compiled binaries. The source code package needs to be compiled and installed before it can be used. The binary distributions need only be unpacked, but they are not available for all platforms.

To install from source code:

gzip -dc canu-1.2.tar.gz | tar -xf -
cd canu-1.1/src
make -j8
cd ..

To install from a binary distribution:

bzip2 -dc canu-1.2*.tar.bz2 | tar -xf -

In both cases, canu is installed directory in canu-1.2/-, for example, canu-1.2/Linux-amd64. You can run the assembler with:

canu-1.2/*/bin/canu

Changes

  • Fix bug of not filtering overlaps sufficiently before input to falcon_sense, leading to fewer corrected reads and a low-quality assembly.

Known Issues

See the issues page for up-to date open issues. The currently known issues are:

  • For large high-coverage genomes it is beneficial to use the fast MHAP mode (generally over 70X).
  • Bogart (unitigger) has false positives in repeat breaking. Currently, the temporary workaround is to increase the minimum overlap size to avoid detecting false repeats caused by short overlaps. Canu will automatically do this for large (>10MB) genomes while the fixed algorithm is tested.
  • For AT/GC rich genomes, it is beneficial to increase the filtering stringency over the default. Specifying corMaxEvidenceErate=0.15 (from the default of 0.2) is generally sufficient.
  • LSF support has limited testing
  • Large memory usage while unitig consensus calling on unitigs over 100MB in size (140Mb contig uses approximate 75GB).
  • Distributed file systems (such as GPFS) causes issues with memory mapped files, slowing down parts of Canu, including meryl (0-mercounts) and falcon-sense (2-correction).

Legal

As Canu is derived from the Celera Assembler, most of the code is GPL licensed. This distribution includes code from Boost, pbdagcon, pbutgcns, and Falcon. For a copyright summary see the README.licenses file as well as individual component licenses included in the repository (boost, falcon, pbdagcon). For more details, see the header in each source file which details its history.

Downloads

Canu v1.1

@skoren skoren released this Mar 9, 2016

These are release notes for Canu version 1.1, which was released on March 11, 2016. Canu is specialized for assembly of single-molecule high-noise sequences. Full documentation can be found at http://canu.readthedocs.org/.

This release provides a stable, tested, and documented version of the software. The binary distributions should work on any relatively recent version of the respective OS. The source code distribution contains everything you need (even the Perl modules!) to create a binary distribution for your own specific OS.

Citation

Installation

Requirements

  • Java SE 8 +
  • GCC 4.5+ (for compilation only)

Users can download Canu as source code or as pre-compiled binaries. The source code package needs to be compiled and installed before it can be used. The binary distributions need only be unpacked, but they are not available for all platforms.

To install from source code:

gzip -dc canu-1.1.tar.gz | tar -xf -
cd canu-1.1/src
make -j8
cd ..

To install from a binary distribution:

bzip2 -dc canu-1.1*.tar.bz2 | tar -xf -

In both cases, canu is installed directory in canu-1.1/-, for example, canu-1.1/Linux-amd64. You can run the assembler with:

canu-1.1/*/bin/canu

Changes

  • Support for reads up to 2Mbp in size (up from 130Kbp).
  • Incorporate MHAP 2.0 which is 5X faster than previous version and has higher specificity
  • Add corMhapSensitivity=fast option which can generate correction overlaps for a human genome in < 2500 CPU hours (full assembly <25,000 CPU hours). This option is recommended for genomes with deeper coverage (60X+).
  • Add GFA output
  • Improve diploid-aware assembly by categorizing output as primary contigs or unmerged bubbles. Annotate repeat and unique contigs in the output.
  • Enable parallel overlap store construction on large genomes
  • Enable minimap as an option for generating overlaps during correction step. Corrected reads are generated as before with falcon_sense.
  • Fix bug using shorter rather than longer reads for corrected reads/consensus computation
  • Fix bug resuming without providing input sequences which would incorrectly set error rates
  • Fix bug in bogart which would demote contained sequences as spurs incorrectly
  • Fix bugs in falcon_sense which would hang when input had N bases and limit corrected reads to 65Kbp
  • Fix falcon_sense support on OSX <10.10.
  • Fix various pipeline bugs

Known Issues

See the issues page for up-to date open issues. The currently known issues are:

  • Canu 1.1 is not backwards compatible with Canu 1.0. If you have an in-process assembly, do not upgrade to Canu 1.1 until it completes.
  • There is a bug with filtering overlaps before passing them to falcon_sense for generating corrected reads on repetitive genomes. If you are assembling large/repetitive genomes (generally >500Mb), you must specify 'corMaxEvidenceErate=0.2' ('corMaxEvidenceErate=0.3' for low-coverage datasets) while the fix is tested.
  • For large high-coverage genomes it is beneficial to use the fast MHAP mode (generally over 70X).
  • Bogart (unitigger) has false positives in repeat breaking. Currently, the temporary workaround is to increase the minimum overlap size to avoid detecting false repeats caused by short overlaps. Canu will automatically do this for large (>100MB) genomes while the fixed algorithm is tested.
  • LSF support has limited testing
  • Large memory usage while unitig consensus calling on unitigs over 100MB in size (140Mb contig uses approximate 75GB).
  • Distributed file systems (such as GPFS) causes issues with memory mapped files, slowing down parts of Canu, including meryl (0-mercounts) and falcon-sense (2-correction).

Legal

As Canu is derived from the Celera Assembler, most of the code is GPL licensed. This distribution includes code from Boost, pbdagcon, pbutgcns, and Falcon. For a copyright summary see the README.licenses file as well as individual component licenses included in the repository (boost, falcon, pbdagcon). For more details, see the header in each source file which details its history.

Downloads

Canu v1.0

@skoren skoren released this Dec 29, 2015 · 950 commits to master since this release

These are release notes for Canu version 1.0, which was released on Dec 29th, 2015. Canu is specialized for assembly of single-molecule high-noise sequences. Full documentation can be found online

This distribution package provides a stable, tested, documented version of the software. The distribution is usable on most Unix-like platforms, and some platforms have pre-compiled binary distributions ready for installation.
The source code package includes full source code, Makefiles, and scripts.

Citation

Compilation and Installation

Requirements

  • Java SE 8 +
  • GCC 4.5+ (for compilation only)

Users can download Canu as source code or as pre-compiled binaries. The source code package needs to be compiled and installed before it can be used. The binary distributions need only be unpacked, but they are not available for all platforms.
To use the source code, execute these commands on any unix-like platform:

gzip -dc canu-1.0.tar.gz | tar -xf -
cd canu-1.0/src
make -j8
cd ..

To use the binary distributions, choose a platform, download that package, then unpack it with some unix command like this:

bzip2 -dc canu-1.0*.tar.bz2 | tar -xf -

In both cases, you can run the assembler with:

canu/*/bin/canu

Known Issues

See the issues page for up-to date open issues. The currently known issues are:

  • LSF support is untested
  • Large memory usage while unitig consensus calling on unitigs over 100MB in size (140Mb contig uses approximate 75GB).
  • Distributed file systems (such as GPFS) causes issues with memory mapped files, slowing down parts of Canu, including meryl (0-mercounts) and falcon-sense (2-correction).

Legal

As Canu is derived from the Celera Assembler, most of the code is GPL licensed. This distribution includes code from Boost, pbdagcon, pbutgcns, and Falcon. For a copyright summary see the README.licenses file as well as individual component licenses included in the repository (boost, falcon, pbdagcon). For more details, see the header in each source file which details its history.

Downloads