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Merqury v1.3

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@arangrhie arangrhie released this 14 Apr 03:01
· 45 commits to master since this release
v1.3
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Learn about vigilant mode.

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.
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