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kff-experiments.md

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Experiments for KFF paper

Dataset accessions

Gallus

SRR105788
SRR105789
SRR105792
SRR105794
SRR197985
SRR197986

Human

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ERR024168
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Steps

Installation of ESS-Compress with KFF support (v3.1)

Requirements

  • Linux operating system (64 bit)
  • Git
  • GCC >= 4.8 or a C++11 capable compiler
  • CMake 3.1+

Install from source:

(Use commit a1ed1c for the experiments in paper)

git clone https://github.com/medvedevgroup/ESSCompress   
cd ESSCompress  
./INSTALL

Alternatively, install from binaries:

Download the latest Linux 64-bit binaries (v3.0).
wget https://github.com/medvedevgroup/ESSCompress/releases/download/v3.1/essCompress-v3.1-linux-64.tar.gz
tar xvzf essCompress-v3.1-linux-64.tar.gz
cd essCompress-v3.1/

Experiments with ESS-Compress and KFF

  1. Put the path to downloaded datasets in fastq.gz format in a file (i.e. for gallus, put them in gallus_lst and for human, human_lst) and generate the KFF file using KMC v3.2.1. The commands look like this: kmc -fq -okff -k32 -ci1 @gallus_lst chicken tmp/ kmc -fq -okff -k32 -ci1 @human_lst human tmp/

  2. We start with human.kff and gallus.kff. To compress these two kff files, use:

bin/essCompress -i gallus.kff
bin/essCompress -i human.kff

By default, it will use single core. To use multiple cores (only BCALM and Blight module of ESS-Compress can use multiple cores),

bin/essCompress -i gallus.kff -t 8   
bin/essCompress -i human.kff -t 8

Final compressed outputs are gallus.compressed.kff and human.compressed.kff.