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README
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README
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/* -------------------------------------------------------------------------- */
/* Copyright (C) 2011, David A. Bader. */
/* All rights reserved. */
/* See COPYING for license. */
/* -------------------------------------------------------------------------- */
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
2) 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.