GRASPx is written in GNU C++ (g++ 4.8.1) and has been tested in
a 64-bit GNU/Linux system. GRASPx contains three components:
'graspx-build', 'graspx-assemble', and 'graspx-map'. 'graspx-build'
is used to index the reads, and is required to run only once for
each sequencing data set. 'graspx-assemble' performs the actual
assembly and output contigs that are homologous to the queries.
'graspx-map' performs the post-mapping that aligns individual reads
back to the predicted contigs.
NOTE: GRASPx currently only supports individual read length up to
255 amino acids and upto 40 millon reads.
To run GRASPx:
Assume that you are in the GRASPx directory
(1) Run 'graspx-build' to generate indexing files:
The indexing files are to be written under './WorkSpace'. You can
specify other indexing files output directories if necessary.
(2) Run 'graspx-assemble' to assemble contigs:
"./bin/graspx-assemble ./examples/sample_query.faa ./examples/sample_reads.faa out_contigs"
The indexing files created under './WorkSpace' is necessary.
The assembled contigs will be written in 'out_contigs' as a
(3) Run 'graspx-map' to align reads to the contigs:
"./bin/graspx-map ./examples/sample_reads.faa out_contigs out_mappings"
The mapping of the reads will be written in 'out_mappings' as
a tab-delimited file as 'read_ID, read_header, contig_header'.
Note: please use '--help' to check out more advanced options.
If you found GRASPx useful, please cite the following papers:
Cuncong Zhong, Youngik Yang, and Shibu Yooseph, "GRASP: Guided
Reference-based Assembly of Short Peptides". (2014) Nucleic Acids Research
Cuncong Zhong, Youngik Yang, and Shibu Yooseph, "GRASPx: an Efficient
Referebce-guided Short Peptide Assembler". Manuscript in preparation
Contact: Cuncong Zhong (firstname.lastname@example.org) or Shibu Yooseph (syooseph.jcvi.org)
The authors would like to acknowledge that GRASP includes (part of) the
BOOST library (htt://www.boost.org) and the libdivsufsort library