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PASQUAL

Our assembler PASQUAL, short for PArallel SeQUence AssembLer, is designed for shared memory parallelism, using OpenMP due to its good tradeoff between performance and programmer productivity.

README

This file contains information about how to install and use PASQUAL, our parallel de novo sequence assembler.

  1. Install

  • Open the Makefile in a text editor. Adapt the settings to your environment, in particular choose your favorite compiler. Save and close.

  • For the machines without SSE support, find "WITH_STNI = 1" in the Makefile and change it to "WITH_STNI = 0".

  • Type make. This builds the object and binary files with default settings.

    Additional flags:

    • INDEX_LENGTH=<U32,U64> to specify the index data type size. Default: U32 When the sequence data sets are smaller than 4GB, use U32 to save memory usage. Otherwise, use U64.
    • TIMING=<0,1> to specify if timing routines are enables or not. Default: 1
  1. Run

Example workflow (adapt to your needs):

iii) Assemble reads contained in reads.fa (read length 50) with a minimum overlap length of 31.

   $> bin/pasqual_omp_u32 or bin/pasqual_omp_u64 --singleread reads.fa -l 50 -t 31
   
   Try pasqual_omp_u32/pasqual_omp_u64 --help for more information.

iv) Contigs are written to output file 'contigs.fa' in FASTA format.