Merqury v1.3

This is Merqury v1.3, compatible and tested with Meryl v1.3.

Download the release source file and extract. No additional compiling or building needed.
Simply add MERQURY as a path variable and we are good to go.

wget https://github.com/marbl/merqury/archive/v1.3.tar.gz
tar -zxvf v1.3.tar.gz
cd merqury-1.3
export MERQURY=$PWD

Add installation dir paths for dependent tools if modules for them are not available: bedtools, samtools, and Rscript to your environment (~/.bash_profile or ~/.profile). source it.

In case your computation environment modules aren't compatible, edit $MERQURY/util/util.sh's check_module to always echo 1.

Release note

• Meryl has much improved in multi-threading and memory management. This will help getting ~3x speed up, especially for the meryl counting and set operations used in Merqury.
• IGV .tdf files are no longer supported. Instead, wiggle (.wig) files are generated.
• Using new meryl syntax.
• Splitting fastq files for kmer counting is deprecated.
• Force R to use cairo engine for plotting to avoid font gobbling and weird plotting issues.
• Minor updates in help messages.

Merqury v1.1

This is Merqury v1.1, an updated version of v1.0 with a few handy features and bug fixes.

This version is compatible and tested with Meryl v1.0.

Download the release source file and extract. No additional compiling or building needed.
Simply add MERQURY as a path variable and we are good to go.

wget https://github.com/marbl/merqury/archive/v1.1.tar.gz
tar -zxvf v1.1.tar.gz
cd merqury-1.1
export MERQURY=$PWD

Add installation dir paths for dependent tools if modules for them are not available: bedtools, samtools, igvtools, and Rscript to your environment (~/.bash_profile or ~/.profile). source it.

New features

• Per sequence entry QV
• Get number of falsely duplicated k-mers
• Additional script to convert bed / hapmers to bigWig

Bug fixes

• Use union-sum instead of union in eval/qv.sh
• Link meryl dbs peroperly
• Lift SLURM dependency

Thanks to everyone who reported bugs here on github or through personal communications.

Merqury v1.0

This version was used to generate the plots and statistics in the preprint:

Arang Rhie, Brian P. Walenz, Sergey Koren, Adam M. Phillippy, Merqury: reference-free quality and phasing assessment for genome assemblies, bioRxiv (2020). doi: https://doi.org/10.1101/2020.03.15.992941

This version is compatible and tested with Meryl v1.0.

Download the release source file and extract. No additional compiling or building needed.
Simply add MERQURY as a path variable and we are good to go.

wget https://github.com/marbl/merqury/archive/v1.0.tar.gz
tar -zxvf merqury-1.0.tar.gz
cd merqury
export MERQURY=$PWD

Add installation dir paths for dependent tools if modules for them are not available: bedtools, samtools, igvtools, and Rscript to your environment (~/.bash_profile or ~/.profile). source it.