Winnowmap 2.03

These are release notes for Winnowmap version 2.03, which was released on May 8, 2021. Full documentation can be found by running winnowmap -h

This release provides a stable, tested, and documented version of the software. Compared to v2.02, the new version includes changes in default parameters to improve runtime.

Installation

Users can download Winnowmap as source code and see README file that specifies a simple installation procedure.

Winnowmap 2.02

These are release notes for Winnowmap version 2.02, which was released on April 28, 2021. Full documentation can be found by running winnowmap -h

This release provides a stable, tested, and documented version of the software. Compared to v2.01, the new version includes minor changes in its minimap2-based backend code. These changes were taken from the recent release of minimap2 v2.18.

Installation

Users can download Winnowmap as source code and see README file that specifies a simple installation procedure.

Winnowmap 2.01

These are release notes for Winnowmap version 2.01, which was released on April 4, 2021. Full documentation can be found by running winnowmap -h

This release provides a stable, tested, and documented version of the software. Compared to v2.0, the new version fixes a bug associated with read alignments getting clipped incorrectly. Thanks to T2T consortium members for highlighting this issue!

Installation

Users can download Winnowmap as source code and see README file that specifies a simple installation procedure.

Winnowmap 2.0

These are release notes for Winnowmap version 2.0, which was released on November 1, 2020. Full documentation can be found by running winnowmap -h

This release provides a stable, tested, and documented version of the software. There are no significant changes compared to v1.11; this release corresponds to Winnowmap2 preprint that is now available through BioRxiv.

Installation

Users can download Winnowmap as source code and see README file that specifies a simple installation procedure.

Winnowmap 1.11

These are release notes for Winnowmap version 1.11, which was released on August 8, 2020. Full documentation can be found by running winnowmap -h

This release provides a stable, tested, and documented version of the software. Compared to v1.1, this version improves runtime by improving load-balance among threads.

Installation

Users can download Winnowmap as source code and see README file that specifies a simple installation procedure.

Winnowmap 1.1

These are release notes for Winnowmap version 1.1, which was released on July 21st, 2020. Full documentation can be found by running winnowmap -h

This release provides a stable, tested, and documented version of the software. Compared to v1.01, this version implements a revised anchor selection algorithm to improve variant calling in repetitive genomic regions.

Installation

Users can download Winnowmap as source code or as pre-compiled linux binaries.

Winnowmap v1.01

Upgraded to meryl k-mer counter; minor improvements / fixes in chaining algorithm; improvement in total runtime.

We recommend git cloning the source code, and compile directly (instructions in README).

Winnowmap 1.0

These are release notes for Winnowmap version 1.0, which was released on February 11th, 2020. Full documentation can be found by running winnowmap -h

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 to create a binary distribution for your own specific OS.

Installation

Users can download Winnowmap as source code or as pre-compiled binaries. The binary distribution is the recommended install method, assuming it is available for your platform. The source code package needs to be compiled and installed before it can be used.

To install from a binary distribution (recommended installation method):

tar -xzf winnowmap-1.0.*.tar.gz
./winnowmap-1.0/winnowmap -h

To install from source code (the file can be named either winnowmap-v1.0.tar.gz or just v1.0.tar.gz, depending on how it is downloaded):

gunzip -dc winnowmap-v1.0.tar.gz | tar -xf -
cd winnowmap
make -j 8
cd ..