• March 27, 2012: PASQUAL website update and PASQUAL v1.0 released.
  • Nov 21, 2011: PASQUAL discussion list moved to pasqual-news.
  • Sep 1, 2011: PASQUAL website update and PASQUAL v0.9 released.


PASQUAL is written in C. Our test environment comprises of two Intel servers. One has two quad-core Intel Xeon X5570 CPUs, the other one four Intel Xeon E7-8870 CPUs with 10 cores each and Hyperthreading.

PASQUAL is compared with four other tools: the de Bruijn graph based assemblers Velvet 1.2.01, ABySS 1.3.2, and SOAPdenovo 1.05, as well as the OLC assembler Edena 3DEV110920 linux64, Except for Edena all tools offer some sort of parallelism and are run in parallel (with shared memory also for the MPI based tool ABySS). All tools take the overlap length as input. In case of Edena and PASQUAL, this is the minimum overlap length, whereas in case of the de Bruijn graph based tools it is the k-mer length. Multiple assembly runs over a range of overlap lengths have to be carried out and the best result chosen.

The parameters used for the various tools are listed below. tau is the minimum length of overlaps or the length of kmers.


$> OMP_NUM_THREADS=<number of threads>

$> velveth <output directory> $tau -fasta < input reads >

$> velvetg <output directory> -exp_cov auto -cov_cutoff auto -scaffolding no -min_contig_lgth 100


$> edena -r <input reads> -M $tau

$> edena -e out.ovl -m $tau


$> abyss-pe np=<number of processes> se-contigs k=$tau se="<input reads>"


==== config file begins ====




f=<input reads>

==== config file ends====

$> SOAPdenovo pregraph -K $tau -p <number of processes> -o <prefix of outputs> -s <config file>

$> SOAPdenovo contig -g <prefix of outputs>


$> OMP_NUM_THREADS=<number of threads>

$> pasqual_omp_u32 --singlereads <input reads> -l <read length> -t $tau --mincontiglen 100